4440223fad68a002964802e0ecf3b1b94cb28503 markd Sat Nov 16 10:11:29 2019 -0800 import of gencode V33 prerelase diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index ebeaecd..d4994b1 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -1,8819 +1,8916 @@ # This contains linkage information between various fields # in various databases. # Define databases used for various organisms set ailMel ailMel1 set allMis allMis1 set ambMex ambMex1 set anaPla anaPla1 set anoCar anoCar1,anoCar2 set anoGam anoGam1,anoGam3 set aotNan aotNan1 set apiMel apiMel1,apiMel2 set aplCal aplCal1 set aptMan aptMan1 set aquChr aquChr2 set astMex astMex1 set balAcu balAcu1 set bisBis bisBis1 set bosTau bosTau2,bosTau3,bosTau4,bosTau5,bosTau6,bosTau7,bosTau8,bosTau9 set braFlo braFlo1,braFlo2 set bruMal bruMal1 set caeAng caeAng1 set caeJap caeJap1,caeJap3,caeJap4 set caePb caePb1,caePb2,caePb3 set caeRem caeRem2,caeRem3,caeRem4 set caeSp11 caeSp111 set calJac calJac1,calJac3 set calMil calMil1 set canFam canFam1,canFam2,canFam3 set casCan casCan1 set cavApe cavApe1 set cavPor cavPor3 set cb cb1,cb3,cb4 set ce ce2,ce4,ce6,ce9,ce10,ce11 set cebCap cebCap1 set cerAty cerAty1 set cerSim cerSim1 set chiLan chiLan1 set choHof choHof1 set chlSab chlSab2 set chrPic chrPic1,chrPic2 set ci ci1,ci2,ci3 set cioSav cioSav1,cioSav2 set colAng colAng1 set cotJap cotJap2 set criGri criGri1,criGriChoV1,criGriChoV2 set danRer danRer3,danRer4,danRer5,danRer6,danRer7,danRer10,danRer11 set dasNov dasNov2,dasNov3 set dipOrd dipOrd1,dipOrd2 set dm dm1,dm2,dm3,dm6 set dp dp2,dp3 set droEre droEre1 set droMoj droMoj1,droMoj2 set droMult droAna1,droAna2,droMoj1,droMoj2,droVir1,droVir2,droEre1,droSim1,droGri1,droPer1,droSec1 set droVir droVir1,droVir2 set droYak droYak1,droYak2 set eboVir eboVir3 set echTel echTel1,echTel2 set equCab equCab1,equCab2,equCab3 set eriEur eriEur1,eriEur2 set eulFla eulFla1 set eulMac eulMac1 set felCat felCat3,felCat4,felCat5,felCat8,felCat9 set ficAlb ficAlb1 set fr fr1,fr2,fr3 set fukDam fukDam1 set gadMor gadMor1 set galGal galGal2,galGal3,galGal4,galGal5,galGal6 set galVar galVar1 set geoFor geoFor1 set melGal melGal1,melGal5 set gasAcu gasAcu1 set gorGor gorGor1,gorGor3,gorGor4,gorGor5 set haeCon haeCon1 set hetGla hetGla1,hetGla2 set hg hg16,hg17,hg18,hg19,hg38 set jacJac jacJac1 set latCha latCha1 set lepOcu lepOcu1 set loxAfr loxAfr3 set manPen manPen1 set macEug macEug1,macEug2 set macNem macNem1 set macFas macFas5 set manLeu manLeu1 set melInc melInc1 set melHap melHap1 set melUnd melUnd1 set mesAur mesAur1 set micMur micMur1,micMur2,micMur3 set micOch micOch1 set mm mm7,mm8,mm9,mm10 set monDom monDom1,monDom4,monDom5 set musFur musFur1 set myoLuc myoLuc1,myoLuc2 set nanGal nanGal1 set nanPar nanPar1 set nasLar nasLar1 set neoSch neoSch1 set nomLeu nomLeu1,nomLeu2,nomLeu3 set ochPri ochPri2,ochPri3 set octDeg octDeg1 set orcOrc orcOrc1 set oreNil oreNil1,oreNil2,oreNil3 set ornAna ornAna1,ornAna2 set oryCun oryCun2 set oryLat oryLat2 set otoGar otoGar1,otoGar3 set oviAri oviAri1,oviAri3,oviAri4 set oxyTri oxyTri2 set panPan panPan1,panPan2 set panManBai panManBai1 set panTro panTro1,panTro2,panTro3,panTro4,panTro5,panTro6 set papAnu papAnu2,papAnu3,papAnu4 set papHam papHam1 set petMar petMar1,petMar2,petMar3 set pelSin pelSin1 set perMan perManBai1 set poeFor poeFor1 set ponAbe ponAbe2,ponAbe3 set priPac priPac1,priPac2,priPac3 set proCap proCap1 set proCoq proCoq1 set pteVam pteVam1 set rheMac rheMac2,rheMac3,rheMac8,rheMac10 set rhiBie rhiBie1 set rhiRox rhiRox1 set rn rn3,rn4,rn5,rn6,regenRn0,regenRn1 set rouAeg rouAeg1 set sacCer sacCer1,sacCer2,sacCer3 set saiBol saiBol1 set sarHar sarHar1 set sorAra sorAra1,sorAra2 set speTri speTri1,speTri2 set susScr susScr1,susScr2,susScr3,susScr11 set staAur staAur1,staAur2 set strPur strPur1,strPur2 set tarSyr tarSyr1,tarSyr2 set taeGut taeGut1,taeGut2 set tetNig tetNig1,tetNig2 set thaSir thaSir1 set triMan triMan1 set tupBel tupBel1 set tupChi tupChi1 set turTru turTru1,turTru2 set vicPac vicPac1,vicPac2 set xenLae xenLae2 set xenTro xenTro1,xenTro2,xenTro3,xenTro7,xenTro9 set xipMac xipMac1 # Define all organism/assembly-specific databases. set gbd $ailMel,$allMis,$ambMex,$anaPla,$anoCar,$anoGam,$aotNan,$apiMel,$aplCal,$aptMan,$aquChr,$astMex,$balAcu,$bisBis,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$canFam,$calJac,$calMil,$casCan,$cavApe,$cavPor,$cb,$ce,$cebCap,$cerAty,$cerSim,$chiLan,$choHof,$chlSab,$chrPic,$ci,$cioSav,$colAng,$cotJap,$criGri,$danRer,$dasNov,$dipOrd,$dm,$dp,$droMult,$droYak,$eboVir,$echTel,$equCab,$eriEur,$eulFla,$eulMac,$felCat,$ficAlb,$fr,$fukDam,$gadMor,$galGal,$gasAcu,$galVar,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$jacJac,$latCha,$lepOcu,$loxAfr,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$melUnd,$mesAur,$micMur,$micOch,$mm,$monDom,$musFur,$myoLuc,$nanGal,$nanPar,$nasLar,$neoSch,$nomLeu,$ochPri,$octDeg,$orcOrc,$oreNil,$ornAna,$oryCun,$oryLat,$otoGar,$oviAri,$oxyTri,$panPan,$panManBai,$panTro,$papAnu,$papHam,$pelSin,$petMar,$perMan,$poeFor,$ponAbe,$priPac,$proCap,$proCoq,$pteVam,$rheMac,$rhiBie,$rhiRox,$rn,$rouAeg,$sacCer,$saiBol,$sarHar,$sorAra,$speTri,$staAur,$strPur,$susScr,$taeGut,$tarSyr,$tetNig,$thaSir,$triMan,$tupBel,$tupChi,$turTru,$vicPac,$xenLae,$xenTro,$xipMac set metaGbd $gbd # Define organism databases based on whole-genome shotgun projects # (Assembly based on WGS project contigs accessioned in Genbank) set wgs $ailMel,$allMis,$aplCal,$balAcu,$bisBis,$bosTau,$bruMal,$calJac,$calMil,$canFam,$cavPor,$choHof,$chrPic,$cioSav,$colAng,$cotJap,$criGri,$dasNov,$dipOrd,$echTel,$eriEur,$eulFla,$eulMac,$felCat,$fr,$galGal,$haeCon,$hetGla,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$micMur,$monDom,$musFur,$myoLuc,$nanPar,$nasLar,$neoSch,$nomLeu,$ochPri,$otoGar,$oryCun,$oryLat,$oviAri,$panPan,$panTro,$proCap,$proCoq,$pteVam,$rn,$sarHar,$sorAra,$speTri,$susScr,$taeGut,$tarSyr,$tetNig,$tupBel,$tupChi,$turTru,$vicPac # Define organism databases for which we build a xenoRefGene track: set xrg $ailMel,$allMis,$anoCar,$anoGam,$aotNan,$aplCal,$aquChr,$balAcu,$bisBis,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$calJac,$calMil,$canFam,$casCan,$cavApe,$cb,$ce,$cebCap,$cerAty,$cerSim,$chlSab,$choHof,$chrPic,$ci,$colAng,$cotJap,$criGri,danRer6,danRer7,danRer10,danRer11,$dasNov,$dipOrd,dm6,$dp,$droMult,$droYak,$echTel,$eriEur,$equCab,$eulFla,$eulMac,$felCat,$ficAlb,$fukDam,$gadMor,$galGal,$galVar,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$latCha,$loxAfr,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$melUnd,$mesAur,$micMur,$micOch,$mm,$monDom,$musFur,$myoLuc,$nanPar,$nasLar,$neoSch,$nomLeu,$ornAna,$ochPri,$orcOrc,$oreNil,$oryCun,$oryLat,$otoGar,$oviAri,$panPan,$panTro,$papAnu,$papHam,$petMar,$ponAbe,$priPac,$proCap,$proCoq,$pteVam,$rheMac,$rhiBie,$rhiRox,$rn,$rouAeg,$saiBol,$sarHar,$sorAra,$speTri,$staAur,$strPur,$susScr,$taeGut,$tarSyr,$thaSir,$triMan,$tupBel,$tupChi,$turTru,$vicPac,$xenLae,$xenTro # Ensembl gene track lists constructed from update procedure set ensGeneDb ailMel1,anaPla1,anoCar2,anoGam3,astMex1,bosTau6,calJac3,canFam2,canFam3,cavApe1,cavPor3,ce10,ce11,chiLan1,chlSab2,choHof1,ci2,ci3,cioSav2,criGri1,criGriChoV1,criGriChoV2,danRer10,danRer11,danRer7,dasNov2,dasNov3,dipOrd1,dipOrd2,dm3,dm6,echTel1,echTel2,equCab2,eriEur1,eriEur2,felCat3,felCat5,ficAlb1,fr2,fr3,fukDam1,gadMor1,galGal3,galGal4,galGal5,gasAcu1,gorGor3,gorGor4,hetGla1,hetGla2,hg16,hg17,hg18,hg19,hg38,jacJac1,latCha1,lepOcu1,loxAfr3,macEug1,melGal1,mesAur1,micMur1,micMur2,micOch1,mm10,mm7,mm8,mm9,monDom5,musFur1,myoLuc2,nanGal1,nomLeu1,nomLeu3,ochPri2,ochPri3,octDeg1,oreNil1,ornAna1,ornAna2,oryCun2,oryLat2,otoGar3,oviAri3,panTro2,panTro4,papAnu2,papAnu3,papAnu4,pelSin1,perManBai1,petMar2,poeFor1,ponAbe2,proCap1,pteVam1,rheMac2,rheMac8,rn3,rn4,rn5,rn6,sacCer3,saiBol1,sarHar1,sorAra1,sorAra2,speTri2,susScr1,susScr11,susScr3,taeGut1,tarSyr1,tetNig2,tupBel1,turTru1,vicPac1,vicPac2,xenTro3,xipMac1 # Databases from the old days when we split some large tables into one table per chrom # Some databases are excluded here because they're excluded from databasesChecked, e.g. cb2, ce3 set oldSplit anoGam1,apiMel2,bosTau3,bosTau4,braFlo1,caeJap1,caePb1,caePb2,caeRem2,caeRem3,canFam1,canFam2,cb1,cb3,cb4,ce10,ce2,ce4,ce6,ce9,danRer3,danRer4,dm1,dm2,dm3,dp3,droSim1,droYak1,droYak2,equCab1,equCab2,fr1,fr2,galGal2,galGal3,gasAcu1,hg16,hg17,hg18,mm10,mm7,mm8,mm9,monDom1,monDom4,panTro1,panTro2,ponAbe2,priPac1,rheMac2,rn3,rn4,sacCer1,sacCer2,sacCer3,strPur2,susScr1,susScr2,taeGut1,tetNig1,tetNig2 set hgSplit hg16,hg17,hg18 # Obsolete archived Ensembl gene tracks set obsoleteEnsGeneDb danRer7,hg16,hg38,rn3 set ensGeneWgs chlSab2,choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,eriEur2,felCat3,gadMor1,micMur1,myoLuc2,ochPri2,ochPri3,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1,vicPac2 set ensGeneScaffold choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,eriEur2,felCat3,gadMor1,micMur1,ochPri2,ochPri3,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1,vicPac2 # Define organism databases for which we host the vegaGenes set vegaGeneDbs hg18,hg19,hg38,mm9,mm10 # Define organism databases for which we build a SNP track: set snpDb127 hg18,bosTau3 set snpDb126 hg18,mm8 set snpDb125 hg17,panTro1,canFam1,rn4 # LS/SNP databases set lsSnpDb hg18,hg19,hg38 # Only consider one of members of gbd at a time. exclusiveSet $gbd # Define other databases that we check set otherDb uniProt,go,hgFixed,proteome,visiGene # Define protein databases (currently not checked) set proteinDb proteins070202,proteins060115,proteins050415,proteins051015,proteins050415,proteins050315,proteins050201,proteins041115,proteins040515,proteins040315,proteins0111,proteins0305,proteins031112,proteins040115,proteins0405,proteins070403,proteins072003,proteins092903,proteins1129 # Define zoo databases (currently not checked) set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3 # Define ucscRetro databases set ucscRetroDb hg19,hg38,mm9,mm10 # Set up list of databases we ignore and those we check. Program # will complain about other databases. databasesChecked $gbd,$otherDb,hgFixed databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp090821,sp080707,sp070202,sp060115,sp051015,sp050415,sp040915,sp040515,sp040315,sp040115,qapushq,mysql-save,hgcentralangie,go070111,go060330,customTracks,customTrash,10Kgenomes,BRfoo,abc,andy,bioCyc070327,bioCyc090623,bioCyc100514,bosTau3Old,ccds,ccds20080404,ccdsNew,ccds_before,ctd,ctd021508,ctdOld,dark,elegansWS176,encpipeline_aamp,encpipeline_beta,encpipeline_galt,encpipeline_kate,encpipeline_prod,encpipeline_test,entrez,euaGli13,eutHer13,fakeDataE0,fanKgTemp,fanKgTemp2,fanTest,fanTest2,gencode,germlineVar_hg18,go040501,go041115,go050521,go050726,go060211,go061219,go080130,goJill,hg15test,hg18kg11,hg18snp130,hg18test,hg19Haps,hg19Patch10,hg19Patch13,hg19Patch9,hg19Patch5,hg19Patch2,hg19Patch2i,hg38Patch2,hg38Patch3,hg38Patch5,hg38Patch6,hg38Patch7,hg38Patch9,hg38Patch11,hg19snp131,hg19snp132,hg19snp134,hg19snp135,hg19snp137,hg19snp138,hg19snp141,hg38snp141,hg19snp142,hg38snp142,hg19snp144,hg38snp144,hg19snp146,hg38snp146,hg19snp147,hg38snp147,hg19snp149,hg38snp149,hg19snp150,hg38snp150,hg19snp151,hg38snp151,mm10snp138,canFam3snp139,bosTau7snp138,bosTau8snp148,susScr3snp138,galGal4snp138,hgcentralgsid,hgcentralrhead,hgcentraltest2,hgcentraltestangie,hiv1,hivgne8,homIni13,homIni14,homIni20,homNea0,homPan20,influenza,information_schema,ismb2004,jkFoo,jorgetest,kgHg17FTemp,kgHg18ATemp,kgMm8ATemp,kgRn3DTemp,markd,markdCcds,markdMGC,membership,metaData_vsmalladi,metadata_krish,mikep,mm9Temp,mm10snp137,mmtv,nonAfr13,oldChoHof1,panTro2snp127,pathway,petMar0,pongo,proteins080707,proteins090821,qa,rah,reactome,rn4UCGenes,rn4snp130,snpCompare,snpFixed,sp100331,sp101005,t18,testMePrivl,tmpBioCychg18,tmpFoo12,tmpUcscGeneshg19,treeFam,uf,ug,vega33,vega40,visiGeneOld,visiGeneXml # Define various non-self chains set chainDest AilMel1,AmbMex1,AncCey1,AnoCar1,AnoCar2,AnoGam1,ApiMel1,ApiMel2,ApiMel3,ApiMel4,AplCal1,AscSuu1,BosTau1,BosTau2,BosTau3,BosTau4,BosTau6,BosTau7,BosTau8,BosTau9,BraFlo1,BraFlo2,BruMal1,BruMal2,BurXyl1,CaeAng1,CaeAng2,CaeJap1,CaeJap3,CaeJap4,CaePb1,CaePb2,CaePb3,CaeRem2,CaeRem3,CaeRem4,CaeSp111,CaeSp51,CalJac1,CalJac3,CalMil1,CanFam1,CanFam2,CanFam3,CanFamPoodle1,CavPor3,Cb1,Cb3,Cb4,Ce2,Ce4,Ce6,Ce9,Ce10,Ce11,ChlSab1,ChlSab2,ChoHof1,ChrPic2,Ci1,Ci2,CioSav2,ColAng1,CriGri1,CriGriChoV1,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,DanRer7,DanRer10,DasNov2,DasNov3,DipOrd1,DirImm1,Dm1,Dm2,Dm3,Dm6,Dp1,Dp2,Dp3,Dp4,DroAlb1,DroAna1,DroAna2,DroAna3,DroBia2,DroBip2,DroEle2,DroEre1,DroEre2,DroEug2,DroFic2,DroGri1,DroGri2,DroKik2,DroMir2,DroMoj1,DroMoj2,DroMoj3,DroPer1,DroPse3,DroRho2,DroSec1,DroSim1,DroSuz1,DroTak2,DroVir1,DroVir2,DroVir3,DroWil1,DroWil2,DroYak1,DroYak2,DroYak3,EchTel1,EquCab1,EquCab2,EquCab3,EriEur1,EriEur2,FalPer1,FelCat3,FelCat4,FelCat5,FelCat8,FelCat9,Fr1,Fr2,Fr3,GadMor1,GalGal2,GalGal3,GalGal4,GalGal5,GalGal6,GalVar1,GasAcu1,GeoFor1,GorGor1,GorGor2,GorGor3,GorGor4,GorGor5,HaeCon1,HaeCon2,HetBac1,HetGla1,HetGla2,Hg16,Hg17,Hg18,Hg19,Hg19Patch2,Hg19Patch5,Hg19Patch9,Hg19Patch10,Hg19Patch13,Hg38Patch2,Hg38Patch3,Hg38Patch5,Hg38Patch6,Hg38Patch7,Hg38Patch9,Hg38Patch11,Hg38,LatCha1,LepWed1,LoaLoa1,LoxAfr2,LoxAfr3,MacEug1,MacEug2,MacFas5,MarVir1,MayZeb1,MelGal1,MelGal5,MelHap1,MelInc1,MelInc2,MelUnd1,MesAur1,MicMur1,MicMur2,MicMur3,MicOch1,Mm5,Mm6,Mm7,Mm8,Mm9,Mm10,Mm10Patch1,Mm10Patch4,MonDom1,MonDom2,MonDom4,MonDom5,MusDom2,MyoLuc1,MyoLuc2,NanPar1,NasLar1,NecAme1,NomLeu1,NomLeu2,NomLeu3,OchPri2,OncVol1,OreNil1,OreNil2,OreNil3,OrnAna1,OrnAna2,OryCun1,OryCun2,OryLat1,OryLat2,OtoGar1,OtoGar3,OviAri1,OviAri3,OviAri4,PanPan1,PanRed1,PanTro1,PanTro2,PanTro3,PanTro4,PanTro5,PanTro6,PapAnu2,PapAnu3,PapHam1,PelSin1,PetMar1,PetMar2,PetMar3,PonAbe2,PonAbe3,PriExs1,PriPac1,PriPac2,PriPac3,ProCap1,ProCoq1,PteVam1,RheMac1,RheMac2,RheMac3,RheMac8,RheMac10,RhiRox1,Rn3,Rn4,Rn5,Rn6,RegenRn0,SaiBol1,SorAra1,SpeTri1,SpeTri2,StrRat1,StrRat2,StrPur1,StrPur2,SusScr1,SusScr2,SusScr3,SusScr11,TaeGut1,TaeGut2,TarSyr1,TarSyr2,TetNig1,TetNig2,TriCas2,TriMan1,TriSpi1,TriSui1,TupBel1,TurTle1,TurTru1,TurTru2,VicPac1,VicPac2,XenLae2,XenTro1,XenTro2,XenTro3,XenTro7,XenTro9 # Define databases that support known genes set kgDb $hg,$mm,rn3 # Older format (KG 2) set kgDb2 hg16,hg17,mm7,mm8,rn3,rn4 # Newer format (KG 3 aka UCSC Genes) set kgDb3 hg18,hg19,hg38,mm9,mm10 # Protein browser databases. set pbDb hg18,hg17,hg16,mm7,mm8,mm9,rn3 set pbDb1 hg17,hg16,mm7,mm8,mm9,rn3 set pbDb2 rn3 set pbDb3 hg16,hg17,hg18 # Define databases that support family browser (gene sorter) set familyDb $hg,$mm,$rn,$ce,$sacCer,$dm # Define databases that support CCDS set ccdsDb hg38,hg19,hg18,hg17,mm8,mm9,mm10 # Magic for tables split between chromosomes set split splitPrefix=chr%\_ # Databases with the tRNAs track set tRNAsDbs ailMel1,anoCar2,bosTau4,bosTau6,caeJap1,caePb1,caePb2,caeRem2,caeRem3,calJac3,canFam2,cavPor3,cb3,ce4,ce6,danRer5,danRer6,danRer7,danRer10,danRer11,equCab1,equCab2,felCat3,felCat4,fr2,fr3,galGal3,gasAcu1,gorGor3,hg18,hg19,hg38,loxAfr3,melGal1,mm9,mm10,monDom5,nomLeu1,ornAna1,oryCun2,oryLat2,oviAri1,oviAri3,panTro2,panTro3,petMar1,ponAbe2,priPac1,rheMac2,rn4,sarHar1,susScr2,taeGut1,taeGut2,tetNig2,xenTro3 # Databases with the CGAP SAGE track set cgapSageDbs hg18,hg19,hg38,mm8 # Define the shared identifiers and the fields they appear in. identifier fishClones "hg38 fishClones IDs linked to BAC Clone IDs" hg38.fishClones.name dupeOk hg38.cloneEndRP11.name minCheck=.03 hg38.cloneEndCTD.name minCheck=.0015 identifier cosmicId "COSMIC entry ID" $hg.cosmic.name $hg.cosmicRaw.cosmic_mutation_id # GO - Gene Ontology Info identifier goAccession external=GO "Gene ontology term accessions. Example - GO:0003574" go.term.acc go.goaPart.goId minCheck=0.999 identifier goAccessionChopped "Gene ontology term accessions without the GO:" go.term.acc chopBefore=GO: dm1.bdgpGeneInfo.go comma minCheck=0.99 dm1.bdgpNonCodingInfo.go comma minCheck=0.99 identifier goId external=GO "Gene ontology term ID's. Shouldn't be used outside of go database" go.term.id go.term2term.term1_id go.term2term.term2_id go.term_audit.term_id go.term_dbxref.term_id go.term_definition.term_id unique go.term_synonym.term_id go.graph_path.term1_id go.graph_path.term2_id identifier goDbXrefId external=GO "Gene ontology database cross-reference" go.dbxref.id go.term_dbxref.dbxref_id # UniProt Related Stuff identifier UniProtId external=UniProt "UniProt(Swiss-Prot/TrEMBL) display ID." uniProt.displayId.val proteome.uniProtAlias.alias minCheck=0.2 proteome.spOldNew.newDisplayId minCheck=0.3 proteome.spOldNew.oldDisplayId minCheck=0.3 proteome.spDisease.displayID minCheck=0.9 go.goaPart.dbObjectSymbol minCheck=0.95 $gbd,!rn4.dupSpMrna.proteinID minCheck=0.80 $gbd,!rn4.dupSpMrna.dupProteinID minCheck=0.50 $kgDb2,!rn4.kgProtAlias.displayID minCheck=0.80 $kgDb2,!rn4.kgSpAlias.alias minCheck=0.20 $kgDb2,!rn4.kgXref.spDisplayID minCheck=0.80 $kgDb3.kgXref.spDisplayID minCheck=0.50 exclude= $kgDb2,!rn4.knownCanonical.protein minCheck=0.80 $gbd.spMrna.spID minCheck=0.80 exclude= dm1.bdgpSwissProt.spSymbol minCheck=0.80 dm1.flyBaseSwissProt.spSymbol minCheck=0.80 identifier ProteomeTaxonId external=Proteome "Proteome Taxon ID" proteome.taxonName.id proteome.spXref3.division minCheck=.90 identifier ProteomeAccession external=Proteome "Proteome Accession" proteome.spXref3.accession dupeOk proteome.hgncXref.uniProt minCheck=.65 identifier UniProtAccession external=UniProt "UniProt(Swiss-Prot/TrEMBL) Accession" uniProt.displayId.acc uniProt.accToKeyword.acc uniProt.accToTaxon.acc uniProt.citation.acc uniProt.comment.acc uniProt.description.acc unique uniProt.extDbRef.acc uniProt.feature.acc uniProt.gene.acc uniProt.geneLogic.acc uniProt.info.acc unique uniProt.otherAcc.acc uniProt.protein.acc unique full proteome.spOldNew.acc minCheck=0.8 proteome.uniProtAlias.acc minCheck=0.9 proteome.spReactomeId.spID minCheck=0.9 proteome.spReactomeEvent.spID minCheck=0.9 $kgDb2,!rn4.kgProtAlias.alias minCheck=0.2 $kgDb2,!rn4.kgSpAlias.spID minCheck=0.2 $kgDb2,!rn4.kgProtMap.qName minCheck=0.9 $kgDb2,!rn4.kgXref.spID minCheck=0.9 $kgDb3.kgSpAlias.spID minCheck=0.50 exclude= $kgDb3.kgXref.spID minCheck=0.50 exclude= $ce.sangerCanonical.protein minCheck=0.8 $ce.sangerGene.proteinID minCheck=0.8 $ce.sangerLinks.protName minCheck=0.8 dm1.bdgpCanonical.protein minCheck=0.9 dm1.bdgpGene.proteinID minCheck=0.9 dm1.bdgpSwissProt.swissProtId minCheck=0.9 dm1.flyBaseSwissProt.swissProtId minCheck=0.9 $sacCer.sgdGene.proteinID minCheck=0.9 $sacCer.sgdCanonical.protein minCheck=0.9 $sacCer.sgdToSwissProt.value minCheck=0.9 go.goaPart.dbObjectId minCheck=0.99 visiGene.gene.uniProt $rn.rgdGene2ToUniProt.value minCheck=0.8 identifier UniProtAuthor "Author ID in UniProt (just use inside UCSC Relationalized UniProt)" uniProt.author.id uniProt.referenceAuthors.author full identifier UniProtReference "Reference (journal) ID in UniProt (just inside UCSC Relationalized)" uniProt.reference.id uniProt.citation.reference full uniProt.referenceAuthors.reference identifier UniProtCitation "Citation ID in UniProt (just use inside UCSC Relationalized UniProt)" uniProt.citation.id uniProt.citationRc.citation identifier UniProtCitationRp "Reference Position Line ID in UniProt (just inside UCSC Relationalized)" uniProt.citationRp.id uniProt.citation.rp full identifier UniProtRcType "Reference Comment Type in UniProt (just inside UCSC Relationalized)" uniProt.rcType.id uniProt.citationRc.rcType full identifier UniProtRcVal "Reference Comment Text in UniProt (just inside UCSC Relationalized)" uniProt.rcVal.id uniProt.citationRc.rcVal full identifier UniProtCommentType "Type of UniProt comment type (just inside UCSC Relationalized)" uniProt.commentType.id uniProt.comment.commentType full identifier UniProtCommentVal "Text of UniProt comment text (just inside UCSC Relationalized)" uniProt.commentVal.id uniProt.comment.commentVal full identifier UniProtExtDb "UniProt(Swiss-Prot/TrEMBL) external database ID (just inside UCSC Relationalized)" uniProt.extDb.id uniProt.extDbRef.extDb full identifier UniProtFeatureClass "Type of UniProt feature class (just inside UCSC Relationalized)" uniProt.featureClass.id uniProt.feature.featureClass full identifier UniProtFeatureType "Type of UniProt feature type (just inside UCSC Relationalized)" uniProt.featureType.id uniProt.feature.featureType full exclude=0 identifier UniProtOrganelle "Type of UniProt organelle ID (just inside UCSC Relationalized)" uniProt.organelle.id uniProt.info.organelle full exclude=0 identifier UniProtKeyword "UniProt(Swiss-Prot/TrEMBL) keyword ID (just inside UCSC Relationalized)" uniProt.keyword.id uniProt.accToKeyword.keyword full identifier ncbiTaxon "NCBI Taxon ID - number for a species. Used by UniProt too" uniProt.taxon.id dupeOk uniProt.accToTaxon.taxon full uniProt.commonName.taxon visiGene.antibody.taxon visiGene.gene.taxon visiGene.genotype.taxon visiGene.specimen.taxon visiGene.lifeTime.taxon visiGene.lifeStageScheme.taxon visiGene.strain.taxon # CGAP SAGE track Stuff identifier cgapSageLibId external=CGAP "ID linking cgapSage and cgapSageLib tables" $cgapSageDbs.cgapSageLib.libId $cgapSageDbs.cgapSage.libIds comma # VisiGene Related Stuff identifier vgFileLocation "Where is that .jpg file? Usually a directory." visiGene.fileLocation.id visiGene.imageFile.fullLocation visiGene.imageFile.thumbLocation identifier vgStrain "Er, what type of mouse is that?" visiGene.strain.id visiGene.genotype.strain exclude=0 identifier vgBodyPart "Brain, eye, cerebral cortex, etc." visiGene.bodyPart.id visiGene.specimen.bodyPart exclude=0 visiGene.expressionLevel.bodyPart exclude=0 identifier vgCellType "Neuron, glia, etc." visiGene.cellType.id visiGene.expressionLevel.cellType exclude=0 identifier vgCellSubtype "More detailed splitting up of cell types. What type of neuron, etc." visiGene.cellSubtype.id visiGene.expressionLevel.cellSubtype exclude=0 identifier vgSliceType "Horizontal, coronal, wholeMount, etc." visiGene.sliceType.id visiGene.preparation.sliceType exclude=0 identifier vgFixation "Fixation conditions - 3% formaldehyde or the like." visiGene.fixation.id visiGene.preparation.fixation exclude=0 identifier vgEmbedding "Embedding media for slices - paraffin, etc." visiGene.embedding.id visiGene.preparation.embedding exclude=0 identifier vgPermeablization "Permeablization conditions" visiGene.permeablization.id visiGene.preparation.permeablization exclude=0 identifier vgContributor "Info on a contributor" visiGene.contributor.id visiGene.submissionContributor.contributor identifier vgJournal "Info on a journal" visiGene.journal.id visiGene.submissionSet.journal exclude=0 identifier vgCopyright "Copyright information" visiGene.copyright.id visiGene.submissionSet.copyright exclude=0 identifier vgSubmissionSource "Source of data - an external database, a contributor, etc." visiGene.submissionSource.id visiGene.submissionSet.submissionSource visiGene.antibodySource.submissionSource exclude=0 identifier vgSubmissionSet "Info on a batch of images submitted at once" visiGene.submissionSet.id visiGene.submissionContributor.submissionSet visiGene.imageFile.submissionSet visiGene.image.submissionSet identifier vgSectionSet "Info on a bunch of sections through some specimen" visiGene.sectionSet.id visiGene.image.sectionSet exclude=0 identifier vgAntibody "Info on an antibody" visiGene.antibody.id visiGene.probe.antibody exclude=0 visiGene.antibodySource.antibody exclude=0 identifier vgBac "Info on a BAC" visiGene.bac.id visiGene.probe.bac exclude=0 identifier vgGene "Info on a gene" visiGene.gene.id visiGene.geneSynonym.gene visiGene.allele.gene visiGene.probe.gene identifier vgAllele "Name of a gene allele" visiGene.allele.id visiGene.genotypeAllele.allele identifier vgGenotype "How different genetically from wild type." visiGene.genotype.id visiGene.genotypeAllele.genotype visiGene.specimen.genotype identifier vgSex "Sex of a specimen" visiGene.sex.id visiGene.specimen.sex exclude=0 identifier vgSpecimen "A biological specimen - something mounted, possibly sliced up" visiGene.specimen.id visiGene.image.specimen identifier vgPreparation "How a specimen is prepared." visiGene.preparation.id visiGene.image.preparation exclude=0 identifier vgProbeType "Type of probe - RNA, antibody, etc." visiGene.probeType.id visiGene.probe.probeType identifier vgProbe "Information on a probe used to stain or hilight image" visiGene.probe.id visiGene.imageProbe.probe visiGene.vgPrbMap.probe identifier vgProbeColor "Color - what color probe is in" visiGene.probeColor.id visiGene.imageProbe.probeColor exclude=0 identifier vgCaption "Caption for image. Id corresponding to text." visiGene.caption.id visiGene.imageFile.caption exclude=0 identifier vgImageFile "A biological image file" visiGene.imageFile.id visiGene.image.imageFile visiGene.imageFileFwd.fromIf visiGene.imageFileFwd.toIf identifier vgImage "Master identifier for a visiGene image. May be just a pane in an image file." visiGene.image.id visiGene.imageProbe.image $kgDb.knownToVisiGene.value identifier vgImageProbe "Association between a probe and an image." visiGene.imageProbe.id visiGene.expressionLevel.imageProbe identifier vgExpressionPattern "Expression pattern - scattered, regional, etc." visiGene.expressionPattern.id visiGene.expressionLevel.expressionPattern exclude=0 identifier vgLifeStageScheme "A scheme for describing stages of development for an organism" visiGene.lifeStageScheme.id visiGene.lifeStage.lifeStageScheme identifier vgPrb "Permanent ID/Probe Sequence table" visiGene.vgPrb.id visiGene.vgPrbMap.vgPrb # Various types of gene predictions in UCSC Genome Browser identifier gencodeGeneNameJun05 dependency "Link together Gencode gene model and class for June 05 Data Freeze" hg17.encodeGencodeGeneJun05.name hg17.gencodeGeneClassJun05.name full unique identifier gencodeGeneNameKnownOct05 dependency "Link together Gencode gene model (Known) and class for Oct 05 Data Freeze" $hg.encodeGencodeGeneKnownOct05.name $hg.gencodeGeneClassOct05.name minCheck=0.88 unique identifier gencodeGeneNamePutativeOct05 dependency "Link together Gencode gene model (Putative) and class for Oct 05 Data Freeze" $hg.encodeGencodeGenePutativeOct05.name $hg.gencodeGeneClassOct05.name minCheck=0.05 unique identifier gencodeGeneNamePseudoOct05 dependency "Link together Gencode gene model (Pseudo) and class for Oct 05 Data Freeze" $hg.encodeGencodeGenePseudoOct05.name $hg.gencodeGeneClassOct05.name minCheck=0.06 unique identifier gencodeGeneNameKnownMar07 dependency "Link together Gencode gene model (Known) and class for Mar 07 Data Version" $hg.encodeGencodeGeneKnownMar07.name $hg.gencodeGeneClassMar07.name minCheck=0.83 unique identifier gencodeGeneNamePutativeMar07 dependency "Link together Gencode gene model (Putative) and class for Mar 07 Data Version" $hg.encodeGencodeGenePutativeMar07.name $hg.gencodeGeneClassMar07.name minCheck=0.10 unique identifier gencodeGeneNamePolymorphicMar07 dependency "Link together Gencode gene model (Polymorphic) and class for Mar 07 Data Version" $hg.encodeGencodeGenePolymorphicMar07.name $hg.gencodeGeneClassMar07.name minCheck=0.006 unique identifier gencodeGeneNamePseudoMar07 dependency "Link together Gencode gene model (Pseudo) and class for Mar 07 Data Version" $hg.encodeGencodeGenePseudoMar07.name $hg.gencodeGeneClassMar07.name minCheck=0.05 unique identifier encodePseudogeneConsensus dependency "Link together Consensus Pseudogenes and class" $hg.encodePseudogeneConsensus.name $hg.encodePseudogeneClass.name minCheck=0.16 unique identifier encodePseudogeneGIS dependency "Link together GIS Pseudogenes and class" $hg.encodePseudogeneGIS.name $hg.encodePseudogeneClass.name minCheck=0.04 unique identifier encodePseudogeneHavana dependency "Link together Havana Pseudogenes and class" $hg.encodePseudogeneHavana.name $hg.encodePseudogeneClass.name minCheck=0.17 unique identifier encodePseudogeneUcsc dependency "Link together Ucsc Retrogenes and class" $hg.encodePseudogeneUcsc.name dupeOk $hg.encodePseudogeneClass.name minCheck=0.22 unique identifier refGeneRetro dependency "Link refGene to ucscRetroInfo" $ucscRetroDb.refGene.name dupeOk hg19.ucscRetroInfo4.refSeq minCheck=0.96 exclude=noRefSeq hg19.ucscRetroInfo5.refSeq minCheck=0.96 exclude=noRefSeq hg38.ucscRetroInfo9.refSeq minCheck=0.96 exclude=noRefSeq mm9.ucscRetroInfo1.refSeq minCheck=0.96 exclude=noRefSeq identifier knownGeneRetro dependency "Link knownGene to ucscRetroInfo" $ucscRetroDb.knownGene.name dupeOk chopAfter=. hg19.ucscRetroInfo4.kgName minCheck=0.96 exclude=noKg chopAfter=. hg19.ucscRetroInfo5.kgName minCheck=0.96 exclude=noKg chopAfter=. hg38.ucscRetroInfo9.kgName minCheck=0.96 exclude=noKg chopAfter=. mm9.ucscRetroInfo1.kgName minCheck=0.94 exclude=noKg chopAfter=. identifier ucscRetroInfo[1,2,4,5,6,9] dependency "Link together Ucsc Retrogenes and ucsc retroGene alignments" $ucscRetroDb.ucscRetroInfo[].name unique $ucscRetroDb.ucscRetroAli[].qName $ucscRetroDb.ucscRetroOrtho[].name $ucscRetroDb.ucscRetroExpressed[].name identifier ucscRetroOrtho[1,2,4,5,6,9] dependency "Link together Ucsc Retrogenes and ucsc retro orthology" $ucscRetroDb.ucscRetroAli[].qName dupeOk $ucscRetroDb.ucscRetroOrtho[].name identifier ucscRetroExtFileId[1,2,4,5,6,9] "External file ID for parent sequences for UCSC Retrogenes" $ucscRetroDb.ucscRetroExtFile[].id $ucscRetroDb.ucscRetroSeq[].extFile identifier ucscRetroSeq4 "Sequences for GenBank sequences used as retrogene parents for version 4" hg19.ucscRetroSeq4.acc unique hg19.ucscRetroCds4.id hg19.ucscRetroAli4.qName chopAfter=- hg19.ucscRetroInfo4.name chopAfter=- identifier ucscRetroSeq5 "Sequences for GenBank sequences used as retrogene parents for version 5" hg19.ucscRetroSeq5.acc unique hg19.ucscRetroCds5.id hg19.ucscRetroAli5.qName chopAfter=- hg19.ucscRetroInfo5.name chopAfter=- identifier ucscRetroSeq9 "Sequences for GenBank sequences used as retrogene parents for version 9" hg38.ucscRetroSeq9.acc unique hg38.ucscRetroCds9.id hg38.ucscRetroAli9.qName chopAfter=- hg38.ucscRetroInfo9.name chopAfter=- identifier ucscRetroSeq1 "Sequences for GenBank sequences used as retrogene parents for version 1" mm9.ucscRetroSeq1.acc unique mm9.ucscRetroCds1.id mm9.ucscRetroAli1.qName chopAfter=- mm9.ucscRetroInfo1.name chopAfter=- identifier ucscRetroSeq2 "Sequences for GenBank sequences used as retrogene parents for version 2" mm10.ucscRetroSeq2.acc unique mm10.ucscRetroCds2.id mm10.ucscRetroAli2.qName chopAfter=- mm10.ucscRetroInfo2.name chopAfter=- identifier ucscRetroSeq6 "Sequences for GenBank sequences used as retrogene parents for version 6" mm10.ucscRetroSeq6.acc unique mm10.ucscRetroCds6.id mm10.ucscRetroAli6.qName chopAfter=- mm10.ucscRetroInfo6.name chopAfter=- identifier encodePseudogeneUcsc2 dependency "Link together Ucsc Pseudogenes and class" $hg.encodePseudogeneUcsc2.name dupeOk $hg.encodePseudogeneClass.name minCheck=0.04 unique identifier encodePseudogeneYale dependency "Link together Yale Pseudogenes and class" $hg.encodePseudogeneYale.name $hg.encodePseudogeneClass.name minCheck=0.16 unique identifier pseudoYale60 "Link together Yale Pseudogenes 60 table with class table" hg19.pseudoYale60.name hg19.pseudoYale60Class.name identifier wgEncodeNhgriBip "Link together Gencode gene model (Known) and class for Jan 2009 Data Version" hg18.wgEncodeNhgriBip.name dupeOk panTro2.wgEncodeNhgriBip.name rheMac2.wgEncodeNhgriBip.name mm9.wgEncodeNhgriBip.name rn4.wgEncodeNhgriBip.name canFam2.wgEncodeNhgriBip.name bosTau4.wgEncodeNhgriBip.name identifier wgEncodeGencodeClassesRel2 "Link together Gencode gene model (Known) and class for Jan 2009 Data Version" hg18.wgEncodeGencodeClassesRel2.name hg18.wgEncodeGencodeAutoRel2.name unique hg18.wgEncodeGencodeManualRel2.name unique hg18.wgEncodeGencodePolyaRel2.name unique identifier wgEncodeGencodeClassesV3 "Link together Gencode gene model (Known) and class for July 2009 Data Version" hg18.wgEncodeGencodeClassesV3.name hg18.wgEncodeGencodeAutoV3.name unique hg18.wgEncodeGencodeManualV3.name unique hg18.wgEncodeGencodePolyaV3.name unique # begin Gencode V7 # = gencode genepreds with joining through wgEncodeGencodeAttrsV7 # wgEncodeGencodeBasicV7 # wgEncodeGencodeCompV7 # wgEncodeGencodePseudoGeneV7 # = gencode genepreds with no associations # wgEncodeGencodePolyaV7 # wgEncodeGencode2wayConsPseudoV7 # gencode association tables (joined through wgEncodeGencodeAttrsV7) #wgEncodeGencodeAttrsV7 #wgEncodeGencodeExonSupportV7 #wgEncodeGencodeGeneSourceV7 #wgEncodeGencodePdbV7 #wgEncodeGencodePubMedV7 #wgEncodeGencodeRefSeqV7 #wgEncodeGencodeTagV7 #wgEncodeGencodeTranscriptSourceV7 #wgEncodeGencodeTranscriptSupportV7 #wgEncodeGencodeUniProtV7 identifier wgEncodeGencodeBasicAttrsV7 "Link together Gencode Basic Table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeAttrsV7.transcriptId hg19.wgEncodeGencodeBasicV7.name identifier wgEncodeGencodeCompAttrsV7 "Link together Gencode Comprehensive Table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeAttrsV7.transcriptId hg19.wgEncodeGencodeCompV7.name identifier wgEncodeGencodePseudoGeneAttrsV7 "Link together Gencode PseudoGene Table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeAttrsV7.transcriptId hg19.wgEncodeGencodePseudoGeneV7.name identifier wgEncodeGencodeExonSupportV7 "Link together Gencode Exon Support table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeExonSupportV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV7 "Link together Gencode Gene Source table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeGeneSourceV7.geneId hg19.wgEncodeGencodeAttrsV7.geneId identifier wgEncodeGencodePdbV7 "Link together Gencode Pdb table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodePdbV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.0397575 identifier wgEncodeGencodePubMedV7 "Link together Gencode Pubmed table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodePubMedV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV7 "Link together Gencode RefSeq table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeRefSeqV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.185827 identifier wgEncodeGencodeTagV7 "Link together Gencode Tag table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeTagV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV7 "Link together Gencode Transcript Source table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeTranscriptSourceV7.transcriptId hg19.wgEncodeGencodeAttrsV7.transcriptId identifier wgEncodeGencodeTranscriptSupportV7 "Link together Gencode Transcript Support table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeTranscriptSupportV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.333503 identifier wgEncodeGencodeUniProtV7 "Link together Gencode UniProt Support table with Attributes table for May 2011 Data Version" hg19.wgEncodeGencodeUniProtV7.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.358209 # end Gencode V7 # begin Gencode V10 # gencode genepreds with no associations # wgEncodeGencodePolyaV10 # wgEncodeGencode2wayConsPseudoV10 # gencode genepreds with joining through wgEncodeGencodeAttrsV10 identifier wgEncodeGencodeBasicAttrsV10 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV10.transcriptId hg19.wgEncodeGencodeBasicV10.name identifier wgEncodeGencodeCompAttrsV10 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV10.transcriptId hg19.wgEncodeGencodeCompV10.name identifier wgEncodeGencodePseudoGeneAttrsV10 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV10.transcriptId hg19.wgEncodeGencodePseudoGeneV10.name # gencode association tables (joined through wgEncodeGencodeAttrsV10) identifier wgEncodeGencodeExonSupportV10 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV10 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV10.geneId hg19.wgEncodeGencodeAttrsV10.geneId identifier wgEncodeGencodePdbV10 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV10 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV10 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.185827 identifier wgEncodeGencodeTagV10 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV10 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV10.transcriptId hg19.wgEncodeGencodeAttrsV10.transcriptId identifier wgEncodeGencodeTranscriptSupportV10 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.30 identifier wgEncodeGencodeTranscriptionSupportLevelV10 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV10 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV10 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.10 # end Gencode V10 # begin Gencode V11 # gencode genepreds with no associations # wgencodegencodepolyav11 # wgEncodeGencode2wayConsPseudoV11 # gencode genepreds with joining through wgEncodeGencodeAttrsV11 identifier wgEncodeGencodeBasicAttrsV11 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV11.transcriptId hg19.wgEncodeGencodeBasicV11.name identifier wgEncodeGencodeCompAttrsV11 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV11.transcriptId hg19.wgEncodeGencodeCompV11.name identifier wgEncodeGencodePseudoGeneAttrsV11 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV11.transcriptId hg19.wgEncodeGencodePseudoGeneV11.name # gencode association tables (joined through wgEncodeGencodeAttrsV11) identifier wgEncodeGencodeExonSupportV11 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV11 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV11.geneId hg19.wgEncodeGencodeAttrsV11.geneId identifier wgEncodeGencodePdbV11 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV11 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV11 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.185827 identifier wgEncodeGencodeTagV11 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV11 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV11.transcriptId hg19.wgEncodeGencodeAttrsV11.transcriptId identifier wgEncodeGencodeTranscriptSupportV11 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.29 identifier wgEncodeGencodeTranscriptionSupportLevelV11 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV11 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV11 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV11.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.10 # end Gencode V11 # begin Gencode V12 # gencode genepreds with no associations # wgEncodeGencodePolyaV12 # wgEncodeGencode2wayConsPseudoV12 # gencode genepreds with joining through wgEncodeGencodeAttrsV12 identifier wgEncodeGencodeBasicAttrsV12 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV12.transcriptId hg19.wgEncodeGencodeBasicV12.name identifier wgEncodeGencodeCompAttrsV12 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV12.transcriptId hg19.wgEncodeGencodeCompV12.name identifier wgEncodeGencodePseudoGeneAttrsV12 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV12.transcriptId hg19.wgEncodeGencodePseudoGeneV12.name # gencode association tables (joined through wgEncodeGencodeAttrsV12) identifier wgEncodeGencodeExonSupportV12 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV12 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV12.geneId hg19.wgEncodeGencodeAttrsV12.geneId identifier wgEncodeGencodePdbV12 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV12 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV12 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.185827 identifier wgEncodeGencodeTagV12 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV12 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV12.transcriptId hg19.wgEncodeGencodeAttrsV12.transcriptId identifier wgEncodeGencodeTranscriptSupportV12 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.29 identifier wgEncodeGencodeTranscriptionSupportLevelV12 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV12 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV12 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV12.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.10 # end Gencode V12 # begin Gencode V14 # gencode genepreds with no associations # wgEncodeGencodePolyaV14 # wgEncodeGencode2wayConsPseudoV14 # gencode genepreds with joining through wgEncodeGencodeAttrsV14 identifier wgEncodeGencodeBasicAttrsV14 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV14.transcriptId hg19.wgEncodeGencodeBasicV14.name identifier wgEncodeGencodeCompAttrsV14 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV14.transcriptId hg19.wgEncodeGencodeCompV14.name identifier wgEncodeGencodePseudoGeneAttrsV14 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV14.transcriptId hg19.wgEncodeGencodePseudoGeneV14.name # gencode association tables (joined through wgEncodeGencodeAttrsV14) identifier wgEncodeGencodeExonSupportV14 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV14 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV14.geneId hg19.wgEncodeGencodeAttrsV14.geneId identifier wgEncodeGencodePdbV14 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV14 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV14 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.18 identifier wgEncodeGencodeTagV14 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV14 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV14.transcriptId hg19.wgEncodeGencodeAttrsV14.transcriptId identifier wgEncodeGencodeTranscriptSupportV14 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelV14 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV14 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV14 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV14.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.10 # end Gencode V14 # begin Gencode V16 # gencode genepreds with no associations # wgEncodeGencodePolyaV16 # wgEncodeGencode2wayConsPseudoV16 # gencode genepreds with joining through wgEncodeGencodeAttrsV16 identifier wgEncodeGencodeBasicAttrsV16 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV16.transcriptId hg19.wgEncodeGencodeBasicV16.name identifier wgEncodeGencodeCompAttrsV16 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV16.transcriptId hg19.wgEncodeGencodeCompV16.name identifier wgEncodeGencodePseudoGeneAttrsV16 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV16.transcriptId hg19.wgEncodeGencodePseudoGeneV16.name # gencode association tables (joined through wgEncodeGencodeAttrsV16) identifier wgEncodeGencodeExonSupportV16 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV16 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV16.geneId hg19.wgEncodeGencodeAttrsV16.geneId identifier wgEncodeGencodePdbV16 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV16 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV16 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagV16 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV16 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV16.transcriptId hg19.wgEncodeGencodeAttrsV16.transcriptId identifier wgEncodeGencodeTranscriptSupportV16 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelV16 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV16 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV16 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV16.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.10 # end Gencode V16 # begin Gencode V17 # gencode genepreds with no associations # wgEncodeGencodePolyaV17 # wgEncodeGencode2wayConsPseudoV17 # gencode genepreds with joining through wgEncodeGencodeAttrsV17 identifier wgEncodeGencodeBasicAttrsV17 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV17.transcriptId hg19.wgEncodeGencodeBasicV17.name identifier wgEncodeGencodeCompAttrsV17 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV17.transcriptId hg19.wgEncodeGencodeCompV17.name identifier wgEncodeGencodePseudoGeneAttrsV17 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV17.transcriptId hg19.wgEncodeGencodePseudoGeneV17.name # gencode association tables (joined through wgEncodeGencodeAttrsV17) identifier wgEncodeGencodeExonSupportV17 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV17 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV17.geneId hg19.wgEncodeGencodeAttrsV17.geneId identifier wgEncodeGencodePdbV17 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV17 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV17 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagV17 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV17 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV17.transcriptId hg19.wgEncodeGencodeAttrsV17.transcriptId identifier wgEncodeGencodeTranscriptSupportV17 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelV17 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV17 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV17 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV17.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV17.transcriptId minCheck=0.10 # end Gencode V17 # begin Gencode V19 # gencode genepreds with no associations # wgEncodeGencodePolyaV19 # wgEncodeGencode2wayConsPseudoV19 # gencode genepreds with joining through wgEncodeGencodeAttrsV19 identifier wgEncodeGencodeBasicAttrsV19 "Link together Gencode Basic Table with Attributes table" hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId hg19,hg38.wgEncodeGencodeBasicV19.name identifier wgEncodeGencodeCompAttrsV19 "Link together Gencode Comprehensive Table with Attributes table" hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId hg19,hg38.wgEncodeGencodeCompV19.name identifier wgEncodeGencodePseudoGeneAttrsV19 "Link together Gencode PseudoGene Table with Attributes table" hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId hg19,hg38.wgEncodeGencodePseudoGeneV19.name # gencode association tables (joined through wgEncodeGencodeAttrsV19) identifier wgEncodeGencodeExonSupportV19 "Link together Gencode Exon Support table with Attributes table" hg19,hg38.wgEncodeGencodeExonSupportV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceV19 "Link together Gencode Gene Source table with Attributes table" hg19,hg38.wgEncodeGencodeGeneSourceV19.geneId hg19,hg38.wgEncodeGencodeAttrsV19.geneId identifier wgEncodeGencodePdbV19 "Link together Gencode Pdb table with Attributes table" hg19,hg38.wgEncodeGencodePdbV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV19 "Link together Gencode Pubmed table with Attributes table" hg19,hg38.wgEncodeGencodePubMedV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV19 "Link together Gencode RefSeq table with Attributes table" hg19,hg38.wgEncodeGencodeRefSeqV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV19 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV19.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.59 identifier wgEncodeGencodeTagV19 "Link together Gencode Tag table with Attributes table" hg19,hg38.wgEncodeGencodeTagV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV19.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV19 "Link together Gencode Transcript Source table with Attributes table" hg19,hg38.wgEncodeGencodeTranscriptSourceV19.transcriptId hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId identifier wgEncodeGencodeTranscriptSupportV19 "Link together Gencode Transcript Support table with Attributes table" hg19,hg38.wgEncodeGencodeTranscriptSupportV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelV19 "Link together Gencode Transcription Support Level table with Attributes table" hg19,hg38.wgEncodeGencodeTranscriptionSupportLevelV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV19 "Link together Gencode UniProt Support table with Attributes table" hg19,hg38.wgEncodeGencodeUniProtV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV19 "Link together Gencode Annotation Remark table with Attributes table" hg19,hg38.wgEncodeGencodeAnnotationRemarkV19.transcriptId dupeOk hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.10 # end Gencode V19 # begin Gencode V20 # gencode genepreds with no associations # wgEncodeGencodePolyaV20 # wgEncodeGencode2wayConsPseudoV20 # gencode genepreds with joining through wgEncodeGencodeAttrsV20 identifier wgEncodeGencodeBasicAttrsV20 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV20.transcriptId hg38.wgEncodeGencodeBasicV20.name identifier wgEncodeGencodeCompAttrsV20 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV20.transcriptId hg38.wgEncodeGencodeCompV20.name identifier wgEncodeGencodePseudoGeneAttrsV20 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV20.transcriptId hg38.wgEncodeGencodePseudoGeneV20.name # gencode association tables (joined through wgEncodeGencodeAttrsV20) identifier wgEncodeGencodeExonSupportV20 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.98 identifier wgEncodeGencodeGeneSourceV20 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV20.geneId hg38.wgEncodeGencodeAttrsV20.geneId identifier wgEncodeGencodePdbV20 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV20 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV20 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagV20 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV20 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV20.transcriptId hg38.wgEncodeGencodeAttrsV20.transcriptId identifier wgEncodeGencodeTranscriptSupportV20 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.81 identifier wgEncodeGencodeTranscriptionSupportLevelV20 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV20 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV20 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV20.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV20.transcriptId minCheck=0.10 # end Gencode V20 # begin Gencode V21 # gencode genepreds with no associations # wgEncodeGencodePolyaV21 # wgEncodeGencode2wayConsPseudoV21 # gencode genepreds with joining through wgEncodeGencodeAttrsV21 identifier wgEncodeGencodeBasicAttrsV21 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV21.transcriptId hg38.wgEncodeGencodeBasicV21.name identifier wgEncodeGencodeCompAttrsV21 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV21.transcriptId hg38.wgEncodeGencodeCompV21.name identifier wgEncodeGencodePseudoGeneAttrsV21 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV21.transcriptId hg38.wgEncodeGencodePseudoGeneV21.name # gencode association tables (joined through wgEncodeGencodeAttrsV21) identifier wgEncodeGencodeExonSupportV21 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.98 identifier wgEncodeGencodeGeneSourceV21 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV21.geneId hg38.wgEncodeGencodeAttrsV21.geneId identifier wgEncodeGencodePdbV21 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV21 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqV21 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagV21 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV21 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV21.transcriptId hg38.wgEncodeGencodeAttrsV21.transcriptId identifier wgEncodeGencodeTranscriptSupportV21 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.81 identifier wgEncodeGencodeTranscriptionSupportLevelV21 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV21 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV21 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV21.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV21.transcriptId minCheck=0.10 # end Gencode V21 # begin Gencode V22 # gencode genepreds with no associations # wgEncodeGencodePolyaV22 # wgEncodeGencode2wayConsPseudoV22 # gencode genepreds with joining through wgEncodeGencodeAttrsV22 identifier wgEncodeGencodeBasicAttrsV22 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV22.transcriptId hg38.wgEncodeGencodeBasicV22.name identifier wgEncodeGencodeCompAttrsV22 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV22.transcriptId hg38.wgEncodeGencodeCompV22.name identifier wgEncodeGencodePseudoGeneAttrsV22 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV22.transcriptId hg38.wgEncodeGencodePseudoGeneV22.name # gencode association tables (joined through wgEncodeGencodeAttrsV22) identifier wgEncodeGencodeExonSupportV22 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.97 identifier wgEncodeGencodeGeneSourceV22 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV22.geneId hg38.wgEncodeGencodeAttrsV22.geneId identifier wgEncodeGencodePdbV22 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV22 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV22 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagV22 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceV22 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV22.transcriptId hg38.wgEncodeGencodeAttrsV22.transcriptId identifier wgEncodeGencodeTranscriptSupportV22 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.22 identifier wgEncodeGencodeTranscriptionSupportLevelV22 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV22 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV22 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV22.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV22.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV22 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV22.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV22.transcriptId minCheck=0.358209 # end Gencode V22 # begin Gencode V23 # gencode genepreds with no associations # wgEncodeGencodePolyaV23 # wgEncodeGencode2wayConsPseudoV23 # gencode genepreds with joining through wgEncodeGencodeAttrsV23 identifier wgEncodeGencodeBasicAttrsV23 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV23.transcriptId hg38.wgEncodeGencodeBasicV23.name identifier wgEncodeGencodeCompAttrsV23 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV23.transcriptId hg38.wgEncodeGencodeCompV23.name identifier wgEncodeGencodePseudoGeneAttrsV23 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV23.transcriptId hg38.wgEncodeGencodePseudoGeneV23.name # gencode association tables (joined through wgEncodeGencodeAttrsV23) identifier wgEncodeGencodeExonSupportV23 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.97 identifier wgEncodeGencodeGeneSourceV23 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV23.geneId hg38.wgEncodeGencodeAttrsV23.geneId identifier wgEncodeGencodePdbV23 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV23 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV23 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV23 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV23.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.8 identifier wgEncodeGencodeTagV23 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV23.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV23 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV23.transcriptId hg38.wgEncodeGencodeAttrsV23.transcriptId identifier wgEncodeGencodeTranscriptSupportV23 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.2297 identifier wgEncodeGencodeTranscriptionSupportLevelV23 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV23 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV23 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV23.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV23.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV23 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV23.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV23.transcriptId minCheck=0.358209 # end Gencode V23 # begin Gencode V24 # gencode genepreds with no associations # wgEncodeGencodePolyaV24 # wgEncodeGencode2wayConsPseudoV24 # gencode genepreds with joining through wgEncodeGencodeAttrsV24 identifier wgEncodeGencodeBasicAttrsV24 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV24.transcriptId hg38.wgEncodeGencodeBasicV24.name identifier wgEncodeGencodeCompAttrsV24 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV24.transcriptId hg38.wgEncodeGencodeCompV24.name identifier wgEncodeGencodePseudoGeneAttrsV24 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV24.transcriptId hg38.wgEncodeGencodePseudoGeneV24.name # gencode association tables (joined through wgEncodeGencodeAttrsV24) identifier wgEncodeGencodeExonSupportV24 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.97 identifier wgEncodeGencodeGeneSourceV24 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV24.geneId hg38.wgEncodeGencodeAttrsV24.geneId identifier wgEncodeGencodePdbV24 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV24 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV24 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV24 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV24.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV24 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV24.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV24 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV24.transcriptId hg38.wgEncodeGencodeAttrsV24.transcriptId identifier wgEncodeGencodeTranscriptSupportV24 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.2285 identifier wgEncodeGencodeTranscriptionSupportLevelV24 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV24 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV24 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV24.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV24.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV24 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV24.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV24.transcriptId minCheck=0.358209 # end Gencode V24 # begin Gencode V25 # gencode genepreds with no associations # wgEncodeGencodePolyaV25 # wgEncodeGencode2wayConsPseudoV25 # gencode genepreds with joining through wgEncodeGencodeAttrsV25 identifier wgEncodeGencodeBasicAttrsV25 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV25.transcriptId hg38.wgEncodeGencodeBasicV25.name identifier wgEncodeGencodeCompAttrsV25 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV25.transcriptId hg38.wgEncodeGencodeCompV25.name identifier wgEncodeGencodePseudoGeneAttrsV25 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV25.transcriptId hg38.wgEncodeGencodePseudoGeneV25.name # gencode association tables (joined through wgEncodeGencodeAttrsV25) identifier wgEncodeGencodeExonSupportV25 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.95 identifier wgEncodeGencodeGeneSourceV25 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV25.geneId hg38.wgEncodeGencodeAttrsV25.geneId identifier wgEncodeGencodePdbV25 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV25 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV25 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV25 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV25.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV25 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV25.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV25 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV25.transcriptId hg38.wgEncodeGencodeAttrsV25.transcriptId identifier wgEncodeGencodeTranscriptSupportV25 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV25 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV25 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV25 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV25.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV25.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV25 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV25.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV25.transcriptId minCheck=0.358209 # end Gencode V25 # begin Gencode V26 # gencode genePred tables with no associations # wgEncodeGencodePolyaV26 # wgEncodeGencode2wayConsPseudoV26 # gencode genePred tables with joining through wgEncodeGencodeAttrsV26 identifier wgEncodeGencodeBasicAttrsV26 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV26.transcriptId hg38.wgEncodeGencodeBasicV26.name identifier wgEncodeGencodeCompAttrsV26 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV26.transcriptId hg38.wgEncodeGencodeCompV26.name identifier wgEncodeGencodePseudoGeneAttrsV26 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV26.transcriptId hg38.wgEncodeGencodePseudoGeneV26.name # gencode association tables (joined through wgEncodeGencodeAttrsV26) identifier wgEncodeGencodeExonSupportV26 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.95 identifier wgEncodeGencodeGeneSourceV26 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV26.geneId hg38.wgEncodeGencodeAttrsV26.geneId identifier wgEncodeGencodePdbV26 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV26 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV26 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV26 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV26.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV26 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV26.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV26 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV26.transcriptId hg38.wgEncodeGencodeAttrsV26.transcriptId identifier wgEncodeGencodeTranscriptSupportV26 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV26 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV26 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV26 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV26.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV26.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV26 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV26.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV26.transcriptId minCheck=0.358209 # end Gencode V26 # begin Gencode V27 # gencode genePred tables with no associations # wgEncodeGencodePolyaV27 # wgEncodeGencode2wayConsPseudoV27 # gencode genePred tables with joining through wgEncodeGencodeAttrsV27 identifier wgEncodeGencodeBasicAttrsV27 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV27.transcriptId hg38.wgEncodeGencodeBasicV27.name identifier wgEncodeGencodeCompAttrsV27 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV27.transcriptId hg38.wgEncodeGencodeCompV27.name identifier wgEncodeGencodePseudoGeneAttrsV27 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV27.transcriptId hg38.wgEncodeGencodePseudoGeneV27.name # gencode association tables (joined through wgEncodeGencodeAttrsV27) identifier wgEncodeGencodeExonSupportV27 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.95 identifier wgEncodeGencodeGeneSourceV27 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV27.geneId hg38.wgEncodeGencodeAttrsV27.geneId identifier wgEncodeGencodePdbV27 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV27 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV27 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV27 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV27.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV27 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV27.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV27 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV27.transcriptId hg38.wgEncodeGencodeAttrsV27.transcriptId identifier wgEncodeGencodeTranscriptSupportV27 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV27 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV27 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV27 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV27.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV27.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV27 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV27.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV27.transcriptId minCheck=0.358209 # end Gencode V27 # begin Gencode V28 # gencode genePred tables with no associations # wgEncodeGencodePolyaV28 # wgEncodeGencode2wayConsPseudoV28 # gencode genePred tables with joining through wgEncodeGencodeAttrsV28 identifier wgEncodeGencodeBasicAttrsV28 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV28.transcriptId hg38.wgEncodeGencodeBasicV28.name identifier wgEncodeGencodeCompAttrsV28 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV28.transcriptId hg38.wgEncodeGencodeCompV28.name identifier wgEncodeGencodePseudoGeneAttrsV28 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV28.transcriptId hg38.wgEncodeGencodePseudoGeneV28.name # gencode association tables (joined through wgEncodeGencodeAttrsV28) identifier wgEncodeGencodeGeneSourceV28 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV28.geneId hg38.wgEncodeGencodeAttrsV28.geneId identifier wgEncodeGencodePdbV28 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV28 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV28 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV28 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV28.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV28 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV28.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV28 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV28.transcriptId hg38.wgEncodeGencodeAttrsV28.transcriptId identifier wgEncodeGencodeTranscriptSupportV28 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV28 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV28 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV28 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV28 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV28.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV28.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportV28 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV28.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV28.transcriptId minCheck=0.95 # end Gencode V28 # begin Gencode V29 # gencode genePred tables with no associations # wgEncodeGencodePolyaV29 # wgEncodeGencode2wayConsPseudoV29 # gencode genePred tables with joining through wgEncodeGencodeAttrsV29 identifier wgEncodeGencodeBasicAttrsV29 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV29.transcriptId hg38.wgEncodeGencodeBasicV29.name identifier wgEncodeGencodeCompAttrsV29 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV29.transcriptId hg38.wgEncodeGencodeCompV29.name identifier wgEncodeGencodePseudoGeneAttrsV29 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV29.transcriptId hg38.wgEncodeGencodePseudoGeneV29.name # gencode association tables (joined through wgEncodeGencodeAttrsV29) identifier wgEncodeGencodeGeneSourceV29 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV29.geneId hg38.wgEncodeGencodeAttrsV29.geneId identifier wgEncodeGencodeGeneSymbolV29 "Link together Gencode gene symbol table with Attributes table" hg38.wgEncodeGencodeGeneSymbolV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV29 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV29 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV29 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV29 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV29.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV29 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV29.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV29 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV29.transcriptId hg38.wgEncodeGencodeAttrsV29.transcriptId identifier wgEncodeGencodeTranscriptSupportV29 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV29 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV29 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV29 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV29 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV29.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV29.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportV29 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV29.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.95 # end Gencode V29 # begin Gencode V30 # gencode genePred tables with no associations # wgEncodeGencodePolyaV30 # wgEncodeGencode2wayConsPseudoV30 # gencode genePred tables with joining through wgEncodeGencodeAttrsV30 identifier wgEncodeGencodeBasicAttrsV30 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV30.transcriptId hg38.wgEncodeGencodeBasicV30.name identifier wgEncodeGencodeCompAttrsV30 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV30.transcriptId hg38.wgEncodeGencodeCompV30.name identifier wgEncodeGencodePseudoGeneAttrsV30 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV30.transcriptId hg38.wgEncodeGencodePseudoGeneV30.name # gencode association tables (joined through wgEncodeGencodeAttrsV30) identifier wgEncodeGencodeGeneSourceV30 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV30.geneId hg38.wgEncodeGencodeAttrsV30.geneId identifier wgEncodeGencodeGeneSymbolV30 "Link together Gencode gene symbol table with Attributes table" hg38.wgEncodeGencodeGeneSymbolV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV30 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV30 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV30 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV30 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV30.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV30 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV30.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV30 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV30.transcriptId hg38.wgEncodeGencodeAttrsV30.transcriptId identifier wgEncodeGencodeTranscriptSupportV30 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV30 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV30 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV30 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV30 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV30.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV30.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportV30 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.95 # end Gencode V30 # begin Gencode V31 # gencode genePred tables with no associations # wgEncodeGencodePolyaV31 # wgEncodeGencode2wayConsPseudoV31 # gencode genePred tables with joining through wgEncodeGencodeAttrsV31 identifier wgEncodeGencodeBasicAttrsV31 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV31.transcriptId hg38.wgEncodeGencodeBasicV31.name identifier wgEncodeGencodeCompAttrsV31 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV31.transcriptId hg38.wgEncodeGencodeCompV31.name identifier wgEncodeGencodePseudoGeneAttrsV31 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV31.transcriptId hg38.wgEncodeGencodePseudoGeneV31.name # gencode association tables (joined through wgEncodeGencodeAttrsV31) identifier wgEncodeGencodeGeneSourceV31 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV31.geneId hg38.wgEncodeGencodeAttrsV31.geneId identifier wgEncodeGencodeGeneSymbolV31 "Link together Gencode gene symbol table with Attributes table" hg38.wgEncodeGencodeGeneSymbolV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV31 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV31 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV31 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV31 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV31.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV31 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.373378 hg38.wgEncodeGencodeRefSeqV31.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV31 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV31.transcriptId hg38.wgEncodeGencodeAttrsV31.transcriptId identifier wgEncodeGencodeTranscriptSupportV31 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV31 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV31 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV31 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV31 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV31.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV31.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportV31 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV31.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.90 # end Gencode V31 # begin Gencode V32 # gencode genePred tables with no associations # wgEncodeGencodePolyaV32 # wgEncodeGencode2wayConsPseudoV32 # gencode genePred tables with joining through wgEncodeGencodeAttrsV32 identifier wgEncodeGencodeBasicAttrsV32 "Link together Gencode Basic Table with Attributes table" hg38.wgEncodeGencodeAttrsV32.transcriptId hg38.wgEncodeGencodeBasicV32.name identifier wgEncodeGencodeCompAttrsV32 "Link together Gencode Comprehensive Table with Attributes table" hg38.wgEncodeGencodeAttrsV32.transcriptId hg38.wgEncodeGencodeCompV32.name identifier wgEncodeGencodePseudoGeneAttrsV32 "Link together Gencode PseudoGene Table with Attributes table" hg38.wgEncodeGencodeAttrsV32.transcriptId hg38.wgEncodeGencodePseudoGeneV32.name # gencode association tables (joined through wgEncodeGencodeAttrsV32) identifier wgEncodeGencodeGeneSourceV32 "Link together Gencode Gene Source table with Attributes table" hg38.wgEncodeGencodeGeneSourceV32.geneId hg38.wgEncodeGencodeAttrsV32.geneId identifier wgEncodeGencodeGeneSymbolV32 "Link together Gencode gene symbol table with Attributes table" hg38.wgEncodeGencodeGeneSymbolV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV32 "Link together Gencode Pdb table with Attributes table" hg38.wgEncodeGencodePdbV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV32 "Link together Gencode Pubmed table with Attributes table" hg38.wgEncodeGencodePubMedV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV32 "Link together Gencode RefSeq table with Attributes table" hg38.wgEncodeGencodeRefSeqV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV32 "Link together Gencode RefSeq table with refGene track" hg38.wgEncodeGencodeRefSeqV32.rnaAcc dupeOk chopAfter=. hg38.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV32 "Link together Gencode Tag table with Attributes table" hg38.wgEncodeGencodeTagV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.36 hg38.wgEncodeGencodeRefSeqV32.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV32 "Link together Gencode Transcript Source table with Attributes table" hg38.wgEncodeGencodeTranscriptSourceV32.transcriptId hg38.wgEncodeGencodeAttrsV32.transcriptId identifier wgEncodeGencodeTranscriptSupportV32 "Link together Gencode Transcript Support table with Attributes table" hg38.wgEncodeGencodeTranscriptSupportV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV32 "Link together Gencode Transcription Support Level table with Attributes table" hg38.wgEncodeGencodeTranscriptionSupportLevelV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV32 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeUniProtV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.35 identifier wgEncodeGencodeAnnotationRemarkV32 "Link together Gencode Annotation Remark table with Attributes table" hg38.wgEncodeGencodeAnnotationRemarkV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV32 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV32.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV32.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportV32 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV32.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.90 # end Gencode V32 +# begin Gencode V33 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaV33 +# wgEncodeGencode2wayConsPseudoV33 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsV33 +identifier wgEncodeGencodeBasicAttrsV33 +"Link together Gencode Basic Table with Attributes table" + hg38.wgEncodeGencodeAttrsV33.transcriptId + hg38.wgEncodeGencodeBasicV33.name + +identifier wgEncodeGencodeCompAttrsV33 +"Link together Gencode Comprehensive Table with Attributes table" + hg38.wgEncodeGencodeAttrsV33.transcriptId + hg38.wgEncodeGencodeCompV33.name + +identifier wgEncodeGencodePseudoGeneAttrsV33 +"Link together Gencode PseudoGene Table with Attributes table" + hg38.wgEncodeGencodeAttrsV33.transcriptId + hg38.wgEncodeGencodePseudoGeneV33.name + +# gencode association tables (joined through wgEncodeGencodeAttrsV33) +identifier wgEncodeGencodeGeneSourceV33 +"Link together Gencode Gene Source table with Attributes table" + hg38.wgEncodeGencodeGeneSourceV33.geneId + hg38.wgEncodeGencodeAttrsV33.geneId + +identifier wgEncodeGencodeGeneSymbolV33 +"Link together Gencode gene symbol table with Attributes table" + hg38.wgEncodeGencodeGeneSymbolV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbV33 +"Link together Gencode Pdb table with Attributes table" + hg38.wgEncodeGencodePdbV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.015 + +identifier wgEncodeGencodePubMedV33 +"Link together Gencode Pubmed table with Attributes table" + hg38.wgEncodeGencodePubMedV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.63 + +identifier wgEncodeGencodeRefSeqV33 +"Link together Gencode RefSeq table with Attributes table" + hg38.wgEncodeGencodeRefSeqV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneV33 +"Link together Gencode RefSeq table with refGene track" + hg38.wgEncodeGencodeRefSeqV33.rnaAcc dupeOk chopAfter=. + hg38.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagV33 +"Link together Gencode Tag table with Attributes table" + hg38.wgEncodeGencodeTagV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.36 + hg38.wgEncodeGencodeRefSeqV33.transcriptId minCheck=0.9 + +identifier wgEncodeGencodeTranscriptSourceV33 +"Link together Gencode Transcript Source table with Attributes table" + hg38.wgEncodeGencodeTranscriptSourceV33.transcriptId + hg38.wgEncodeGencodeAttrsV33.transcriptId + +identifier wgEncodeGencodeTranscriptSupportV33 +"Link together Gencode Transcript Support table with Attributes table" + hg38.wgEncodeGencodeTranscriptSupportV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.20 + +identifier wgEncodeGencodeTranscriptionSupportLevelV33 +"Link together Gencode Transcription Support Level table with Attributes table" + hg38.wgEncodeGencodeTranscriptionSupportLevelV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtV33 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeUniProtV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeAnnotationRemarkV33 +"Link together Gencode Annotation Remark table with Attributes table" + hg38.wgEncodeGencodeAnnotationRemarkV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneV33 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeEntrezGeneV33.transcriptId dupeOk + hg38.wgEncodeGencodeEntrezGeneV33.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeExonSupportV33 +"Link together Gencode Exon Support table with Attributes table" + hg38.wgEncodeGencodeExonSupportV33.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.90 + +# end Gencode V33 + + # begin Gencode V24lift37 # gencode genepreds with no associations # wgEncodeGencodePolyaV24lift37 # wgEncodeGencode2wayConsPseudoV24lift37 # gencode genepreds with joining through wgEncodeGencodeAttrsV24lift37 identifier wgEncodeGencodeBasicAttrsV24lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV24lift37.transcriptId hg19.wgEncodeGencodeBasicV24lift37.name identifier wgEncodeGencodeCompAttrsV24lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV24lift37.transcriptId hg19.wgEncodeGencodeCompV24lift37.name identifier wgEncodeGencodePseudoGeneAttrsV24lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV24lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV24lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV24lift37) identifier wgEncodeGencodeExonSupportV24lift37 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.97 identifier wgEncodeGencodeGeneSourceV24lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV24lift37.geneId hg19.wgEncodeGencodeAttrsV24lift37.geneId identifier wgEncodeGencodePdbV24lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV24lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV24lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV24lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV24lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV24lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV24lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV24lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV24lift37.transcriptId hg19.wgEncodeGencodeAttrsV24lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV24lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.2297 identifier wgEncodeGencodeTranscriptionSupportLevelV24lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV24lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV24lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV24lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV24lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV24lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV24lift37.transcriptId minCheck=0.358209 # end Gencode V24lift37 # begin Gencode V26lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV26lift37 # wgEncodeGencode2wayConsPseudoV26lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV26lift37 identifier wgEncodeGencodeBasicAttrsV26lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV26lift37.transcriptId hg19.wgEncodeGencodeBasicV26lift37.name identifier wgEncodeGencodeCompAttrsV26lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV26lift37.transcriptId hg19.wgEncodeGencodeCompV26lift37.name identifier wgEncodeGencodePseudoGeneAttrsV26lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV26lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV26lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV26lift37) identifier wgEncodeGencodeGeneSourceV26lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV26lift37.geneId hg19.wgEncodeGencodeAttrsV26lift37.geneId identifier wgEncodeGencodePdbV26lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedV26lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV26lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV26lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV26lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV26lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV26lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV26lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV26lift37.transcriptId hg19.wgEncodeGencodeAttrsV26lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV26lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV26lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV26lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV26lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV26lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV26lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV26lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV26lift37.transcriptId minCheck=0.358209 # end Gencode V26lift37 # begin Gencode V27lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV27lift37 # wgEncodeGencode2wayConsPseudoV27lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV27lift37 identifier wgEncodeGencodeBasicAttrsV27lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV27lift37.transcriptId hg19.wgEncodeGencodeBasicV27lift37.name identifier wgEncodeGencodeCompAttrsV27lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV27lift37.transcriptId hg19.wgEncodeGencodeCompV27lift37.name identifier wgEncodeGencodePseudoGeneAttrsV27lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV27lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV27lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV27lift37) identifier wgEncodeGencodeExonSupportV27lift37 "Link together Gencode Exon Support table with Attributes table" hg19.wgEncodeGencodeExonSupportV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.95 identifier wgEncodeGencodeGeneSourceV27lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV27lift37.geneId hg19.wgEncodeGencodeAttrsV27lift37.geneId identifier wgEncodeGencodePdbV27lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV27lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV27lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV27lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV27lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV27lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV27lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV27lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV27lift37.transcriptId hg19.wgEncodeGencodeAttrsV27lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV27lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV27lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV27lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV27lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV27lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV27lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV27lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV27lift37.transcriptId minCheck=0.358209 # end Gencode V27lift37 # begin Gencode V28lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV28lift37 # wgEncodeGencode2wayConsPseudoV28lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV28lift37 identifier wgEncodeGencodeBasicAttrsV28lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV28lift37.transcriptId hg19.wgEncodeGencodeBasicV28lift37.name identifier wgEncodeGencodeCompAttrsV28lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV28lift37.transcriptId hg19.wgEncodeGencodeCompV28lift37.name identifier wgEncodeGencodePseudoGeneAttrsV28lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV28lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV28lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV28lift37) identifier wgEncodeGencodeGeneSourceV28lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV28lift37.geneId hg19.wgEncodeGencodeAttrsV28lift37.geneId identifier wgEncodeGencodePdbV28lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV28lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV28lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV28lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV28lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV28lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV28lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV28lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV28lift37.transcriptId hg19.wgEncodeGencodeAttrsV28lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV28lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV28lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV28lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV28lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV28lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV28lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV28lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV28lift37.transcriptId minCheck=0.358209 # end Gencode V28lift37 # begin Gencode V29lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV29lift37 # wgEncodeGencode2wayConsPseudoV29lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV29lift37 identifier wgEncodeGencodeBasicAttrsV29lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV29lift37.transcriptId hg19.wgEncodeGencodeBasicV29lift37.name identifier wgEncodeGencodeCompAttrsV29lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV29lift37.transcriptId hg19.wgEncodeGencodeCompV29lift37.name identifier wgEncodeGencodePseudoGeneAttrsV29lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV29lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV29lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV29lift37) identifier wgEncodeGencodeGeneSourceV29lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV29lift37.geneId hg19.wgEncodeGencodeAttrsV29lift37.geneId identifier wgEncodeGencodeGeneSymbolV29lift37 "Link together Gencode gene symbol table with Attributes table" hg19.wgEncodeGencodeGeneSymbolV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV29lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV29lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV29lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV29lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV29lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV29lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV29lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV29lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV29lift37.transcriptId hg19.wgEncodeGencodeAttrsV29lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV29lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV29lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV29lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV29lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV29lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV29lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV29lift37.transcriptId minCheck=0.358209 # end Gencode V29lift37 # begin Gencode V30lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV30lift37 # wgEncodeGencode2wayConsPseudoV30lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV30lift37 identifier wgEncodeGencodeBasicAttrsV30lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV30lift37.transcriptId hg19.wgEncodeGencodeBasicV30lift37.name identifier wgEncodeGencodeCompAttrsV30lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV30lift37.transcriptId hg19.wgEncodeGencodeCompV30lift37.name identifier wgEncodeGencodePseudoGeneAttrsV30lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV30lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV30lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV30lift37) identifier wgEncodeGencodeGeneSourceV30lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV30lift37.geneId hg19.wgEncodeGencodeAttrsV30lift37.geneId identifier wgEncodeGencodeGeneSymbolV30lift37 "Link together Gencode gene symbol table with Attributes table" hg19.wgEncodeGencodeGeneSymbolV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV30lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV30lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV30lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV30lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV30lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV30lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.373378 hg19.wgEncodeGencodeRefSeqV30lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV30lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV30lift37.transcriptId hg19.wgEncodeGencodeAttrsV30lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV30lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV30lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV30lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV30lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV30lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV30lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV30lift37.transcriptId minCheck=0.358209 # end Gencode V30lift37 # begin Gencode V31lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV31lift37 # wgEncodeGencode2wayConsPseudoV31lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV31lift37 identifier wgEncodeGencodeBasicAttrsV31lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV31lift37.transcriptId hg19.wgEncodeGencodeBasicV31lift37.name identifier wgEncodeGencodeCompAttrsV31lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV31lift37.transcriptId hg19.wgEncodeGencodeCompV31lift37.name identifier wgEncodeGencodePseudoGeneAttrsV31lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV31lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV31lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV31lift37) identifier wgEncodeGencodeGeneSourceV31lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV31lift37.geneId hg19.wgEncodeGencodeAttrsV31lift37.geneId identifier wgEncodeGencodeGeneSymbolV31lift37 "Link together Gencode gene symbol table with Attributes table" hg19.wgEncodeGencodeGeneSymbolV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV31lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV31lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV31lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV31lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV31lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV31lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.36 hg19.wgEncodeGencodeRefSeqV31lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV31lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV31lift37.transcriptId hg19.wgEncodeGencodeAttrsV31lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV31lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV31lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV31lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.35 identifier wgEncodeGencodeAnnotationRemarkV31lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV31lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV31lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV31lift37.transcriptId minCheck=0.35 # end Gencode V31lift37 # begin Gencode V32lift37 # gencode genePred tables with no associations # wgEncodeGencodePolyaV32lift37 # wgEncodeGencode2wayConsPseudoV32lift37 # gencode genePred tables with joining through wgEncodeGencodeAttrsV32lift37 identifier wgEncodeGencodeBasicAttrsV32lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV32lift37.transcriptId hg19.wgEncodeGencodeBasicV32lift37.name identifier wgEncodeGencodeCompAttrsV32lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV32lift37.transcriptId hg19.wgEncodeGencodeCompV32lift37.name identifier wgEncodeGencodePseudoGeneAttrsV32lift37 "Link together Gencode PseudoGene Table with Attributes table" hg19.wgEncodeGencodeAttrsV32lift37.transcriptId hg19.wgEncodeGencodePseudoGeneV32lift37.name # gencode association tables (joined through wgEncodeGencodeAttrsV32lift37) identifier wgEncodeGencodeGeneSourceV32lift37 "Link together Gencode Gene Source table with Attributes table" hg19.wgEncodeGencodeGeneSourceV32lift37.geneId hg19.wgEncodeGencodeAttrsV32lift37.geneId identifier wgEncodeGencodeGeneSymbolV32lift37 "Link together Gencode gene symbol table with Attributes table" hg19.wgEncodeGencodeGeneSymbolV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbV32lift37 "Link together Gencode Pdb table with Attributes table" hg19.wgEncodeGencodePdbV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedV32lift37 "Link together Gencode Pubmed table with Attributes table" hg19.wgEncodeGencodePubMedV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqV32lift37 "Link together Gencode RefSeq table with Attributes table" hg19.wgEncodeGencodeRefSeqV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneV32lift37 "Link together Gencode RefSeq table with refGene track" hg19.wgEncodeGencodeRefSeqV32lift37.rnaAcc dupeOk chopAfter=. hg19.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagV32lift37 "Link together Gencode Tag table with Attributes table" hg19.wgEncodeGencodeTagV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.36 hg19.wgEncodeGencodeRefSeqV32lift37.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceV32lift37 "Link together Gencode Transcript Source table with Attributes table" hg19.wgEncodeGencodeTranscriptSourceV32lift37.transcriptId hg19.wgEncodeGencodeAttrsV32lift37.transcriptId identifier wgEncodeGencodeTranscriptSupportV32lift37 "Link together Gencode Transcript Support table with Attributes table" hg19.wgEncodeGencodeTranscriptSupportV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelV32lift37 "Link together Gencode Transcription Support Level table with Attributes table" hg19.wgEncodeGencodeTranscriptionSupportLevelV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtV32lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.35 identifier wgEncodeGencodeAnnotationRemarkV32lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV32lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV32lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV32lift37.transcriptId minCheck=0.35 # end Gencode V32lift37 # begin Gencode VM2 # gencode genepreds with no associations # wgEncodeGencodePolyaVM2 # wgEncodeGencode2wayConsPseudoVM2 # gencode genepreds with joining through wgEncodeGencodeAttrsVM2 identifier wgEncodeGencodeBasicAttrsVM2 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM2.transcriptId mm10.wgEncodeGencodeBasicVM2.name identifier wgEncodeGencodeCompAttrsVM2 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM2.transcriptId mm10.wgEncodeGencodeCompVM2.name identifier wgEncodeGencodePseudoGeneAttrsVM2 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM2.transcriptId mm10.wgEncodeGencodePseudoGeneVM2.name # gencode association tables (joined through wgEncodeGencodeAttrsVM2) identifier wgEncodeGencodeExonSupportVM2 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.98202 identifier wgEncodeGencodeGeneSourceVM2 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM2.geneId mm10.wgEncodeGencodeAttrsVM2.geneId identifier wgEncodeGencodePdbVM2 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedVM2 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM2 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM2 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM2 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM2.transcriptId mm10.wgEncodeGencodeAttrsVM2.transcriptId identifier wgEncodeGencodeTranscriptSupportVM2 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM2 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM2 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM2 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM2.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM2.transcriptId minCheck=0.10 # end Gencode VM2 # begin Gencode VM3 # gencode genepreds with no associations # wgEncodeGencodePolyaVM3 # wgEncodeGencode2wayConsPseudoVM3 # gencode genepreds with joining through wgEncodeGencodeAttrsVM3 identifier wgEncodeGencodeBasicAttrsVM3 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM3.transcriptId mm10.wgEncodeGencodeBasicVM3.name identifier wgEncodeGencodeCompAttrsVM3 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM3.transcriptId mm10.wgEncodeGencodeCompVM3.name identifier wgEncodeGencodePseudoGeneAttrsVM3 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM3.transcriptId mm10.wgEncodeGencodePseudoGeneVM3.name # gencode association tables (joined through wgEncodeGencodeAttrsVM3) identifier wgEncodeGencodeExonSupportVM3 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.97 identifier wgEncodeGencodeGeneSourceVM3 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM3.geneId mm10.wgEncodeGencodeAttrsVM3.geneId identifier wgEncodeGencodePdbVM3 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedVM3 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM3 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM3 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM3 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM3.transcriptId mm10.wgEncodeGencodeAttrsVM3.transcriptId identifier wgEncodeGencodeTranscriptSupportVM3 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM3 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM3 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM3 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM3.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM3.transcriptId minCheck=0.10 # end Gencode VM3 # begin Gencode VM4 # gencode genepreds with no associations # wgEncodeGencodePolyaVM4 # wgEncodeGencode2wayConsPseudoVM4 # gencode genepreds with joining through wgEncodeGencodeAttrsVM4 identifier wgEncodeGencodeBasicAttrsVM4 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM4.transcriptId mm10.wgEncodeGencodeBasicVM4.name identifier wgEncodeGencodeCompAttrsVM4 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM4.transcriptId mm10.wgEncodeGencodeCompVM4.name identifier wgEncodeGencodePseudoGeneAttrsVM4 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM4.transcriptId mm10.wgEncodeGencodePseudoGeneVM4.name # gencode association tables (joined through wgEncodeGencodeAttrsVM4) identifier wgEncodeGencodeExonSupportVM4 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.97 identifier wgEncodeGencodeGeneSourceVM4 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM4.geneId mm10.wgEncodeGencodeAttrsVM4.geneId identifier wgEncodeGencodePdbVM4 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.02 identifier wgEncodeGencodePubMedVM4 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM4 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM4 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM4 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM4.transcriptId mm10.wgEncodeGencodeAttrsVM4.transcriptId identifier wgEncodeGencodeTranscriptSupportVM4 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM4 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM4 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM4 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM4.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM4.transcriptId minCheck=0.10 # end Gencode VM4 # begin Gencode VM7 # gencode genepreds with no associations # wgEncodeGencodePolyaVM7 # wgEncodeGencode2wayConsPseudoVM7 # gencode genepreds with joining through wgEncodeGencodeAttrsVM7 identifier wgEncodeGencodeBasicAttrsVM7 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM7.transcriptId mm10.wgEncodeGencodeBasicVM7.name identifier wgEncodeGencodeCompAttrsVM7 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM7.transcriptId mm10.wgEncodeGencodeCompVM7.name identifier wgEncodeGencodePseudoGeneAttrsVM7 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM7.transcriptId mm10.wgEncodeGencodePseudoGeneVM7.name # gencode association tables (joined through wgEncodeGencodeAttrsVM7) identifier wgEncodeGencodeExonSupportVM7 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.96 identifier wgEncodeGencodeGeneSourceVM7 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM7.geneId mm10.wgEncodeGencodeAttrsVM7.geneId identifier wgEncodeGencodePdbVM7 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.017 identifier wgEncodeGencodePubMedVM7 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM7 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM7 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM7 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM7.transcriptId mm10.wgEncodeGencodeAttrsVM7.transcriptId identifier wgEncodeGencodeTranscriptSupportVM7 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM7 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM7 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM7 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM7.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM7.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM7 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM7.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM7.transcriptId minCheck=0.358209 # end Gencode VM7 # begin Gencode VM8 # gencode genepreds with no associations # wgEncodeGencodePolyaVM8 # wgEncodeGencode2wayConsPseudoVM8 # gencode genepreds with joining through wgEncodeGencodeAttrsVM8 identifier wgEncodeGencodeBasicAttrsVM8 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM8.transcriptId mm10.wgEncodeGencodeBasicVM8.name identifier wgEncodeGencodeCompAttrsVM8 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM8.transcriptId mm10.wgEncodeGencodeCompVM8.name identifier wgEncodeGencodePseudoGeneAttrsVM8 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM8.transcriptId mm10.wgEncodeGencodePseudoGeneVM8.name # gencode association tables (joined through wgEncodeGencodeAttrsVM8) identifier wgEncodeGencodeExonSupportVM8 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.96 identifier wgEncodeGencodeGeneSourceVM8 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM8.geneId mm10.wgEncodeGencodeAttrsVM8.geneId identifier wgEncodeGencodePdbVM8 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.017 identifier wgEncodeGencodePubMedVM8 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM8 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM8 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM8 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM8.transcriptId mm10.wgEncodeGencodeAttrsVM8.transcriptId identifier wgEncodeGencodeTranscriptSupportVM8 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM8 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM8 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM8 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM8.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM8.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM8 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM8.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM8.transcriptId minCheck=0.358209 # end Gencode VM8 # begin Gencode VM9 # gencode genepreds with no associations # wgEncodeGencodePolyaVM9 # wgEncodeGencode2wayConsPseudoVM9 # gencode genepreds with joining through wgEncodeGencodeAttrsVM9 identifier wgEncodeGencodeBasicAttrsVM9 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM9.transcriptId mm10.wgEncodeGencodeBasicVM9.name identifier wgEncodeGencodeCompAttrsVM9 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM9.transcriptId mm10.wgEncodeGencodeCompVM9.name identifier wgEncodeGencodePseudoGeneAttrsVM9 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM9.transcriptId mm10.wgEncodeGencodePseudoGeneVM9.name # gencode association tables (joined through wgEncodeGencodeAttrsVM9) identifier wgEncodeGencodeExonSupportVM9 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.94 identifier wgEncodeGencodeGeneSourceVM9 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM9.geneId mm10.wgEncodeGencodeAttrsVM9.geneId identifier wgEncodeGencodePdbVM9 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.017 identifier wgEncodeGencodePubMedVM9 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM9 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM9 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM9 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM9.transcriptId mm10.wgEncodeGencodeAttrsVM9.transcriptId identifier wgEncodeGencodeTranscriptSupportVM9 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM9 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM9 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM9 "link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM9.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM9.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM9 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM9.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM9.transcriptId minCheck=0.358209 # end Gencode VM9 # begin Gencode VM10 # gencode genepreds with no associations # wgEncodeGencodePolyaVM10 # wgEncodeGencode2wayConsPseudoVM10 # gencode genepreds with joining through wgEncodeGencodeAttrsVM10 identifier wgEncodeGencodeBasicAttrsVM10 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM10.transcriptId mm10.wgEncodeGencodeBasicVM10.name identifier wgEncodeGencodeCompAttrsVM10 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM10.transcriptId mm10.wgEncodeGencodeCompVM10.name identifier wgEncodeGencodePseudoGeneAttrsVM10 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM10.transcriptId mm10.wgEncodeGencodePseudoGeneVM10.name # gencode association tables (joined through wgEncodeGencodeAttrsVM10) identifier wgEncodeGencodeExonSupportVM10 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.94 identifier wgEncodeGencodeGeneSourceVM10 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM10.geneId mm10.wgEncodeGencodeAttrsVM10.geneId identifier wgEncodeGencodePdbVM10 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.017 identifier wgEncodeGencodePubMedVM10 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM10 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM10 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM10 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM10.transcriptId mm10.wgEncodeGencodeAttrsVM10.transcriptId identifier wgEncodeGencodeTranscriptSupportVM10 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM10 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM10 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM10 "link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM10.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM10.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM10 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM10.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM10.transcriptId minCheck=0.358209 # end Gencode VM10 # begin Gencode VM11 # gencode genepreds with no associations # wgEncodeGencodePolyaVM11 # wgEncodeGencode2wayConsPseudoVM11 # gencode genepreds with joining through wgEncodeGencodeAttrsVM11 identifier wgEncodeGencodeBasicAttrsVM11 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM11.transcriptId mm10.wgEncodeGencodeBasicVM11.name identifier wgEncodeGencodeCompAttrsVM11 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM11.transcriptId mm10.wgEncodeGencodeCompVM11.name identifier wgEncodeGencodePseudoGeneAttrsVM11 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM11.transcriptId mm10.wgEncodeGencodePseudoGeneVM11.name # gencode association tables (joined through wgEncodeGencodeAttrsVM11) identifier wgEncodeGencodeExonSupportVM11 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.94 identifier wgEncodeGencodeGeneSourceVM11 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM11.geneId mm10.wgEncodeGencodeAttrsVM11.geneId identifier wgEncodeGencodePdbVM11 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.017 identifier wgEncodeGencodePubMedVM11 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.635488 identifier wgEncodeGencodeRefSeqVM11 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.05 identifier wgEncodeGencodeTagVM11 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.373378 identifier wgEncodeGencodeTranscriptSourceVM11 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM11.transcriptId mm10.wgEncodeGencodeAttrsVM11.transcriptId identifier wgEncodeGencodeTranscriptSupportVM11 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.25 identifier wgEncodeGencodeTranscriptionSupportLevelVM11 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM11 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM11 "link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM11.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM11.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM11 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM11.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM11.transcriptId minCheck=0.358209 # end Gencode VM11 # begin Gencode VM13 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM13 # wgEncodeGencode2wayConsPseudoVM13 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM13 identifier wgEncodeGencodeBasicAttrsVM13 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM13.transcriptId mm10.wgEncodeGencodeBasicVM13.name identifier wgEncodeGencodeCompAttrsVM13 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM13.transcriptId mm10.wgEncodeGencodeCompVM13.name identifier wgEncodeGencodePseudoGeneAttrsVM13 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM13.transcriptId mm10.wgEncodeGencodePseudoGeneVM13.name # gencode association tables (joined through wgEncodeGencodeAttrsVM13) identifier wgEncodeGencodeExonSupportVM13 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.90 identifier wgEncodeGencodeGeneSourceVM13 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM13.geneId mm10.wgEncodeGencodeAttrsVM13.geneId identifier wgEncodeGencodePdbVM13 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM13 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM13 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM13 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM13.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM13 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.373378 mm10.wgEncodeGencodeRefSeqVM13.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM13 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM13.transcriptId mm10.wgEncodeGencodeAttrsVM13.transcriptId identifier wgEncodeGencodeTranscriptSupportVM13 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM13 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM13 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM13 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM13.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM13.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM13 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM13.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM13.transcriptId minCheck=0.358209 # end Gencode VM13 # begin Gencode VM14 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM14 # wgEncodeGencode2wayConsPseudoVM14 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM14 identifier wgEncodeGencodeBasicAttrsVM14 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM14.transcriptId mm10.wgEncodeGencodeBasicVM14.name identifier wgEncodeGencodeCompAttrsVM14 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM14.transcriptId mm10.wgEncodeGencodeCompVM14.name identifier wgEncodeGencodePseudoGeneAttrsVM14 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM14.transcriptId mm10.wgEncodeGencodePseudoGeneVM14.name # gencode association tables (joined through wgEncodeGencodeAttrsVM14) identifier wgEncodeGencodeExonSupportVM14 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.95 identifier wgEncodeGencodeGeneSourceVM14 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM14.geneId mm10.wgEncodeGencodeAttrsVM14.geneId identifier wgEncodeGencodePdbVM14 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM14 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM14 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM14 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM14.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM14 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.373378 mm10.wgEncodeGencodeRefSeqVM14.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM14 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM14.transcriptId mm10.wgEncodeGencodeAttrsVM14.transcriptId identifier wgEncodeGencodeTranscriptSupportVM14 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM14 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM14 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM14 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM14.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM14.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM14 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM14.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM14.transcriptId minCheck=0.358209 # end Gencode VM14 # begin Gencode VM16 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM16 # wgEncodeGencode2wayConsPseudoVM16 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM16 identifier wgEncodeGencodeBasicAttrsVM16 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM16.transcriptId mm10.wgEncodeGencodeBasicVM16.name identifier wgEncodeGencodeCompAttrsVM16 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM16.transcriptId mm10.wgEncodeGencodeCompVM16.name identifier wgEncodeGencodePseudoGeneAttrsVM16 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM16.transcriptId mm10.wgEncodeGencodePseudoGeneVM16.name # gencode association tables (joined through wgEncodeGencodeAttrsVM16) identifier wgEncodeGencodeGeneSourceVM16 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM16.geneId mm10.wgEncodeGencodeAttrsVM16.geneId identifier wgEncodeGencodePdbVM16 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM16 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM16 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM16 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM16.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM16 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.373378 mm10.wgEncodeGencodeRefSeqVM16.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM16 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM16.transcriptId mm10.wgEncodeGencodeAttrsVM16.transcriptId identifier wgEncodeGencodeTranscriptSupportVM16 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM16 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM16 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM16 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM16 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM16.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM16.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportVM16 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM16.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM16.transcriptId minCheck=0.95 # end Gencode VM16 # begin Gencode VM18 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM18 # wgEncodeGencode2wayConsPseudoVM18 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM18 identifier wgEncodeGencodeBasicAttrsVM18 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM18.transcriptId mm10.wgEncodeGencodeBasicVM18.name identifier wgEncodeGencodeCompAttrsVM18 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM18.transcriptId mm10.wgEncodeGencodeCompVM18.name identifier wgEncodeGencodePseudoGeneAttrsVM18 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM18.transcriptId mm10.wgEncodeGencodePseudoGeneVM18.name # gencode association tables (joined through wgEncodeGencodeAttrsVM18) identifier wgEncodeGencodeGeneSourceVM18 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM18.geneId mm10.wgEncodeGencodeAttrsVM18.geneId identifier wgEncodeGencodePdbVM18 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM18 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM18 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM18 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM18.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM18 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.373378 mm10.wgEncodeGencodeRefSeqVM18.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM18 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM18.transcriptId mm10.wgEncodeGencodeAttrsVM18.transcriptId identifier wgEncodeGencodeTranscriptSupportVM18 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM18 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM18 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM18 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM18 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM18.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM18.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportVM18 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM18.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.95 # end Gencode VM18 # begin Gencode VM21 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM21 # wgEncodeGencode2wayConsPseudoVM21 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM21 identifier wgEncodeGencodeBasicAttrsVM21 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM21.transcriptId mm10.wgEncodeGencodeBasicVM21.name identifier wgEncodeGencodeCompAttrsVM21 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM21.transcriptId mm10.wgEncodeGencodeCompVM21.name identifier wgEncodeGencodePseudoGeneAttrsVM21 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM21.transcriptId mm10.wgEncodeGencodePseudoGeneVM21.name # gencode association tables (joined through wgEncodeGencodeAttrsVM21) identifier wgEncodeGencodeGeneSourceVM21 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM21.geneId mm10.wgEncodeGencodeAttrsVM21.geneId identifier wgEncodeGencodeGeneSymbolVM21 "Link together Gencode gene symbol table with Attributes table" mm10.wgEncodeGencodeGeneSymbolVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbVM21 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM21 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM21 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM21 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM21.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM21 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.373378 mm10.wgEncodeGencodeRefSeqVM21.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM21 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM21.transcriptId mm10.wgEncodeGencodeAttrsVM21.transcriptId identifier wgEncodeGencodeTranscriptSupportVM21 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM21 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM21 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkVM21 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM21 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM21.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM21.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportVM21 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.95 # end Gencode VM21 # begin Gencode VM22 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM22 # wgEncodeGencode2wayConsPseudoVM22 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM22 identifier wgEncodeGencodeBasicAttrsVM22 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM22.transcriptId mm10.wgEncodeGencodeBasicVM22.name identifier wgEncodeGencodeCompAttrsVM22 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM22.transcriptId mm10.wgEncodeGencodeCompVM22.name identifier wgEncodeGencodePseudoGeneAttrsVM22 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM22.transcriptId mm10.wgEncodeGencodePseudoGeneVM22.name # gencode association tables (joined through wgEncodeGencodeAttrsVM22) identifier wgEncodeGencodeGeneSourceVM22 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM22.geneId mm10.wgEncodeGencodeAttrsVM22.geneId identifier wgEncodeGencodeGeneSymbolVM22 "Link together Gencode gene symbol table with Attributes table" mm10.wgEncodeGencodeGeneSymbolVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbVM22 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM22 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM22 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM22 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM22.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM22 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.36 mm10.wgEncodeGencodeRefSeqVM22.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM22 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM22.transcriptId mm10.wgEncodeGencodeAttrsVM22.transcriptId identifier wgEncodeGencodeTranscriptSupportVM22 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM22 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM22 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.35 identifier wgEncodeGencodeAnnotationRemarkVM22 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM22 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM22.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM22.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportVM22 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM22.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.90 # end Gencode VM22 # begin Gencode VM23 # gencode genePred tables with no associations # wgEncodeGencodePolyaVM23 # wgEncodeGencode2wayConsPseudoVM23 # gencode genePred tables with joining through wgEncodeGencodeAttrsVM23 identifier wgEncodeGencodeBasicAttrsVM23 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM23.transcriptId mm10.wgEncodeGencodeBasicVM23.name identifier wgEncodeGencodeCompAttrsVM23 "Link together Gencode Comprehensive Table with Attributes table" mm10.wgEncodeGencodeAttrsVM23.transcriptId mm10.wgEncodeGencodeCompVM23.name identifier wgEncodeGencodePseudoGeneAttrsVM23 "Link together Gencode PseudoGene Table with Attributes table" mm10.wgEncodeGencodeAttrsVM23.transcriptId mm10.wgEncodeGencodePseudoGeneVM23.name # gencode association tables (joined through wgEncodeGencodeAttrsVM23) identifier wgEncodeGencodeGeneSourceVM23 "Link together Gencode Gene Source table with Attributes table" mm10.wgEncodeGencodeGeneSourceVM23.geneId mm10.wgEncodeGencodeAttrsVM23.geneId identifier wgEncodeGencodeGeneSymbolVM23 "Link together Gencode gene symbol table with Attributes table" mm10.wgEncodeGencodeGeneSymbolVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.20 identifier wgEncodeGencodePdbVM23 "Link together Gencode Pdb table with Attributes table" mm10.wgEncodeGencodePdbVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.015 identifier wgEncodeGencodePubMedVM23 "Link together Gencode Pubmed table with Attributes table" mm10.wgEncodeGencodePubMedVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.63 identifier wgEncodeGencodeRefSeqVM23 "Link together Gencode RefSeq table with Attributes table" mm10.wgEncodeGencodeRefSeqVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.05 identifier wgEncodeGencodeRefSeqToRefGeneVM23 "Link together Gencode RefSeq table with refGene track" mm10.wgEncodeGencodeRefSeqVM23.rnaAcc dupeOk chopAfter=. mm10.refGene.name minCheck=0.77 identifier wgEncodeGencodeTagVM23 "Link together Gencode Tag table with Attributes table" mm10.wgEncodeGencodeTagVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.36 mm10.wgEncodeGencodeRefSeqVM23.transcriptId minCheck=0.9 identifier wgEncodeGencodeTranscriptSourceVM23 "Link together Gencode Transcript Source table with Attributes table" mm10.wgEncodeGencodeTranscriptSourceVM23.transcriptId mm10.wgEncodeGencodeAttrsVM23.transcriptId identifier wgEncodeGencodeTranscriptSupportVM23 "Link together Gencode Transcript Support table with Attributes table" mm10.wgEncodeGencodeTranscriptSupportVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.20 identifier wgEncodeGencodeTranscriptionSupportLevelVM23 "Link together Gencode Transcription Support Level table with Attributes table" mm10.wgEncodeGencodeTranscriptionSupportLevelVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.30 identifier wgEncodeGencodeUniProtVM23 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeUniProtVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.35 identifier wgEncodeGencodeAnnotationRemarkVM23 "Link together Gencode Annotation Remark table with Attributes table" mm10.wgEncodeGencodeAnnotationRemarkVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM23 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM23.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM23.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportVM23 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM23.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.90 # end Gencode VM23 identifier wgEncodeGencodeClassesV3Hg19 "Link together Gencode gene model (Known) and class for July 2009 Data Version" hg19.wgEncodeGencodeClassesV3.name hg19.wgEncodeGencodeAutoV3.name unique hg19.wgEncodeGencodeManualV3.name unique hg19.wgEncodeGencodePolyaV3.name unique identifier acemblyName dependency "Link together Acembly gene model structure and peptide." $hg,$mm.acembly.name $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90 hg17.acemblyPep.name unique minCheck=0.63 $hg,$mm.acemblyClass.name full unique identifier ECgeneName dependency "Link together EC gene predicted gene structure and peptide" $gbd.ECgene.name $gbd.ECgenePep.name unique identifier geneidName dependency "Link together geneid predicted gene structure and peptide" $gbd.geneid.name $gbd.geneidPep.name full unique identifier genscanName dependency "Link together genscan predicted gene structure and peptide" $gbd.genscan.name $gbd.genscanPep.name full unique identifier jgiName dependency "Link together jgi predicted gene structure and peptide" $gbd.jgiGene.name $gbd.jgiPep.name unique minCheck=0.9 identifier softberryGeneName dependency "Link together Fshgene++ gene structure, pepdide, and homolog" $gbd.softberryGene.name $gbd.softberryPep.name full unique $gbd.softberryHom.name unique identifier twinscanName dependency "Link together twinscan predicted gene structure and peptide" $gbd.twinscan.name $gbd.twinscanPep.name full unique identifier nscanName dependency "Link together nscan predicted gene structure and peptide" $gbd.nscanGene.name $gbd.nscanPep.name unique identifier nscanPasaName dependency "Link together nscan predicted gene structure (PASA) and peptide" $gbd.nscanPasaGene.name $gbd.nscanPasaPep.name unique identifier augustusHintsName dependency "Link together augustusHints predicted gene structure and peptide" $gbd.augustusHints.name $gbd.augustusHintsPep.name chopBefore=. full unique identifier augustusXRAName dependency "Link together augustusXRA predicted gene structure and peptide" $gbd.augustusXRA.name $gbd.augustusXRAPep.name chopBefore=. full unique identifier augustusAbinitioName dependency "Link together augustusAbinitio predicted gene structure and peptide" $gbd.augustusAbinitio.name $gbd.augustusAbinitioPep.name chopBefore=. full unique identifier vegaGeneId external=VegaGene "Link together various VEGA curated gene annotation" $vegaGeneDbs.vegaGtp.transcript $vegaGeneDbs.vegaGene.name $vegaGeneDbs.vegaPseudoGene.name $vegaGeneDbs.vegaPep.name identifier vegaName "Link together various VEGA human curated gene annotation" $gbd.vegaInfo.transcriptId $gbd.vegaGene.name $gbd.vegaPseudoGene.name identifier vegaGeneName typeOf=vegaName dependency "Link together VEGA predicted gene structure and peptide" $gbd.vegaGene.name danRer5.vegaPep.name unique minCheck=0.72 identifier vegaZfishName "Link together various VEGA zebrafish curated gene annotation" $gbd.vegaInfoZfish.transcriptId identifier vegaGeneZfishName typeOf=vegaZfishName dependency "Link together Zebrafish VEGA predicted gene structure additional information" $danRer.vegaGene.name $danRer.vegaInfoZfish.transcriptId minCheck=0.99 $danRer.vegaToCloneId.transcriptId minCheck=0.99 identifier vegaPseudoZfishName typeOf=vegaZfishName "Link together VEGA pseudogene and other info." $danRer.vegaPseudoGene.name identifier vegaPseudoGeneZfishName typeOf=vegaPseudoZfishName dependency "Link together Zebrafish VEGA predicted gene structure additional information" $danRer.vegaPseudoGene.name $danRer.vegaInfoZfish.transcriptId minCheck=0.004 $danRer.vegaToCloneId.transcriptId minCheck=0.004 identifier vegaPseudogeneName typeOf=vegaName "Link together VEGA pseudogene and other info." $gbd.vegaPseudoGene.name #identifier pseudoGeneName #"Link together pseudo predicted gene structure and peptide" # $hg.pseudoMrna.qName dupeOk # hg16,hg17,hg18.pseudoGeneLink.name minCheck=0.99 identifier mrnaBlastzName "Link together mrnaBlastz and pseudoMrna" $hg.mrnaBlastz.qName dupeOk $hg,!hg16.pseudoMrna.qName hg16.pseudoMrna.qName minCheck=0.76 identifier decipherId "DECIPHER CNVs ID" $hg.decipher.name dupeOk $hg.decipherRaw.id $hg.knownToDecipher.value $hg.knownCanonToDecipher.value identifier decipherSnvsId "DECIPHER SNVs ID" $hg.decipherSnvs.name dupeOk $hg.decipherSnvsRaw.id # Microarray stuff. identifier agilentHumanProbeId external=agilent fuzzy "Agilent Human CGH/CNV array probe ID" $hg.agilentCgh1x1m.name $hg.agilentHrd1x1m.name $hg.agilentCghSnp2x400k.name $hg.agilentCgh2x400k.name $hg.agilentCghSnpCancer4x180k.name $hg.agilentCghSnp4x180k.name $hg.agilentCgh4x180k.name $hg.agilentCgh8x60k.name $hg.agilentCgh244a.name $hg.agilentCgh105a.name $hg.agilentCgh44k.name identifier agilentMouseProbeId external=agilent fuzzy "Agilent Mouse CGH/CNV array probe ID" $mm.agilentCgh1x1m.name $mm.agilentCgh4x180k.name $mm.agilentCgh244a.name $mm.agilentCgh105a.name identifier agilentRatProbeId external=agilent fuzzy "Agilent Rat CGH/CNV array probe ID" $rn.agilentCgh1x1m.name $rn.agilentCgh4x180k.name $rn.agilentCgh244a.name $rn.agilentCgh105a.name identifier sestanBrainAtlasId "Sample IDs for the Sestan brain atlas array." hgFixed.sestanBrainAtlasExps.id $hg.sestanBrainAtlas.expIds comma full $hg.sestanBrainAtlas.expScores comma indexOf full identifier affyMouseExonSampleId "Sample IDs for Affymetrix all mouse exon array." hgFixed.affyMouseExonTissuesAllExps.id $mm.affyExonTissues.expIds comma full $mm.affyExonTissues.expScores comma indexOf full identifier affyRatExonSampleId "Sample IDs for Affymetrix all rat exon array." hgFixed.affyRatExonTissuesAllExps.id $rn.affyExonTissues.expIds comma full $rn.affyExonTissues.expScores comma indexOf full identifier affyExonTissuesGsId "UCSC Gene IDs for affyExonTissuesGs." $hg.affyExonTissuesGs.name $hg.knownGene.name minCheck=0.95 identifier affyExonTissuesGsMedianId "UCSC Gene IDs for affyExonTissuesGsMedian." $hg.affyExonTissuesGsMedian.name $hg.knownGene.name minCheck=0.95 identifier affyExonTissuesGsMedianDistId "UCSC Gene IDs for affyExonTissuesGsMedianDist." $hg.affyExonTissuesGsMedianDist.query dupeOk $hg.affyExonTissuesGsMedianDist.target $hg.knownGene.name minCheck=0.95 identifier gnfHumanAtlas2 "Novartis GNF Human gene probe ID" hgFixed.gnfHumanAtlas2All.name hgFixed.gnfHumanAtlas2AllRatio.name unique hgFixed.gnfHumanAtlas2Median.name full unique hgFixed.gnfHumanAtlas2MedianRatio.name unique hgFixed.gladHumESRatio.name unique hgFixed.gladHumES.name hgFixed.gladHumESOtherData.name $hg.knownToGnfAtlas2.value $hg.gnfAtlas2.name $hg.affyGnf1h.qName identifier gnfMouseAtlas2 "Novartis GNF Mouse gene probe ID" hgFixed.gnfMouseAtlas2All.name hgFixed.gnfMouseAtlas2AllRatio.name unique hgFixed.gnfMouseAtlas2Median.name full unique hgFixed.gnfMouseAtlas2MedianRatio.name unique $mm.knownToGnf1m.value $mm.gnfAtlas2.name $mm.affyGnf1m.qName identifier gnfMOE430v2 "Novartis GNF Mouse gene probe ID" hgFixed.gnfMOE430v2All.name hgFixed.gnfMOE430v2AllRatio.name unique hgFixed.gnfMOE430v2Median.name full unique hgFixed.gnfMOE430v2MedianRatio.name unique $mm.knownToGnfMOE430v2.value $mm.gnfMOE430v2.name $mm.affyMOE430v2.qName identifier gnfRatAtlas2 "Novartis GNF Rat gene probe ID" hgFixed.gnfRatAtlas2All.name hgFixed.gnfRatAtlas2AllRatio.name unique hgFixed.gnfRatAtlas2Median.name full unique hgFixed.gnfRatAtlas2MedianRatio.name unique $rn.knownToGnfRatAtlas2.value $rn.rgdGene2ToGnfRatAtlas2.value $rn.gnfAtlas2.name $rn.affyU34A.qName identifier affyZonWildType "Affymetrix Zebrafish chip Zon Lab data probe ID" hgFixed.zebrafishZonWTAll.name hgFixed.zebrafishZonWTAllRatio.name unique hgFixed.zebrafishZonWTMedian.name unique hgFixed.zebrafishZonWTMedianRatio.name. unique $danRer.ensToAffyZebrafish.name $danRer.ensToAffyZonWildType.name $danRer.affyZonWildType.name $danRer.affyZebrafish.qName danRer5.affyZebrafishConsensus.qName identifier affyZonWildTypeDanRer5 "Affymetrix Zebrafish chip Zon Lab data probe ID Consensus" danRer5.affyZonWildType.name dupeOk danRer5.affyZebrafishConsensus.qName identifier affyTargetZonWildTypeDanRer5 "Affymetrix Zebrafish chip Zon Lab data probe ID Target" danRer5.affyTargetZonWildType.name dupeOk danRer5.affyZebrafishTarget.qName identifier affyU95 "Affymetrix Human U95 chip identifiers" $hg.affyU95.qName dupeOk $hg.affyRatio.name $hg.knownToU95.value identifier affyU133WithChop # chopBefore and chopAfter needed for hg16, 17 and 18. "Affymetrix Human U133 chip identifiers" hg16,hg17,hg18.affyU133.qName dupeOk chopBefore=U133A: chopBefore=U133B: chopAfter=; hg16,hg17,hg18.knownToU133.value identifier affyU133 "Affymetrix Human U133 chip identifiers" $hg,!hg16,!hg17,!hg18.affyU133.qName dupeOk $hg,!hg16,!hg17,!hg18.knownToU133.value identifier affyU133Plus2 "Affymetrix Human U133 chip identifiers" $hg.affyU133Plus2.qName dupeOk $hg.knownToU133Plus2.value identifier affyU74 "Affymetrix Mouse U74 chip identifiers" $mm.affyU74.qName dupeOk $mm.affyGnfU74A.name $mm.affyGnfU74B.name $mm.affyGnfU74C.name $mm.knownToU74.value identifier affyMOE430 "Affymetrix Mouse MOE430 chip identifiers" $mm.affyMOE430.qName dupeOk $mm.knownToMOE430.value $mm.knownToMOE430A.value $mm.rinnSex.name hgFixed.mouseRinnSex.name minCheck=0.96 hgFixed.mouseRinnSexMedian.name minCheck=0.96 hgFixed.mouseRinnSexRatio.name minCheck=0.97 hgFixed.mouseRinnSexMedianRatio.name minCheck=0.97 identifier affyRAE230 "Affymetrix Rat RAE230 chip identifiers" $rn.affyRAE230.qName dupeOk $rn,!rn4.knownToRAE230.value $rn.rgdGene2ToRAE230.value identifier affyU34A "Affymetrix Rat U34A chip identifiers" $rn.affyU34A.qName dupeOk $rn,!rn4.knownToU34A.value $rn.rgdGene2ToU34A.value identifier illuminaWG6 "Illumina WG-6 3.0 Probe set identifiers" $hg.illuminaProbes.name dupeOk $hg.illuminaProbesAlign.qName full $hg.illuminaProbesSeq.id minCheck=0.8 identifier kimWormGeneId "Identifiers for Kim-lab worm genes" hgFixed.kimWormLifeAllRatio.name hgFixed.kimWormLifeMedianRatio.name full unique $ce.sangerToKim.value minCheck=0.6 identifier nci60SampleId "Identifiers of NCI 60 Cell lines for expression experiments" hgFixed.nci60Exps.id $hg.nci60.expIds comma full $hg.nci60.expScores comma indexOf full identifier rosettaChr22SampleId "Identifiers for samples used in Rosetta chromosome 22 public experiments" hgFixed.rosettaExps.name hgFixed.rosChr22Dat.expName identifier gnfHumanAtlas2SampleId "Identifiers of RNA samples used in GNF Human Expression Atlas 2" hgFixed.gnfHumanAtlas2AllExps.id hgFixed.gnfHumanAtlas2All.expScores comma indexOf full hgFixed.gnfHumanAtlas2AllRatio.expScores comma indexOf full identifier gnfHumanAtlas2MedianSampleId "Identifiers of pooled RNA samples used in GNF Human Expression Atlas 2" hgFixed.gnfHumanAtlas2MedianExps.id hgFixed.gnfHumanAtlas2Median.expScores comma indexOf full hgFixed.gnfHumanAtlas2MedianRatio.expScores comma indexOf full $hg.gnfAtlas2.expScores comma indexOf full identifier gnfMouseAtlas2SampleId "Identifiers of RNA samples used in GNF Mouse Expression Atlas 2" hgFixed.gnfMouseAtlas2AllExps.id hgFixed.gnfMouseAtlas2All.expScores comma indexOf full hgFixed.gnfMouseAtlas2AllRatio.expScores comma indexOf full identifier gnfMouseAtlas2MedianSampleId "Identifiers of pooled RNA samples used in GNF Mouse Expression Atlas 2" hgFixed.gnfMouseAtlas2MedianExps.id hgFixed.gnfMouseAtlas2Median.expScores comma indexOf full hgFixed.gnfMouseAtlas2MedianRatio.expScores comma indexOf full $mm.gnfAtlas2.expScores comma indexOf full identifier gnfRatAtlas2SampleId "Identifiers of RNA samples used in GNF Rat Expression Atlas 2" hgFixed.gnfRatAtlas2AllExps.id hgFixed.gnfRatAtlas2All.expScores comma indexOf full hgFixed.gnfRatAtlas2AllRatio.expScores comma indexOf full identifier gnfRatAtlas2MedianSampleId "Identifiers of pooled RNA samples used in GNF Rat Expression Atlas 2" hgFixed.gnfRatAtlas2MedianExps.id hgFixed.gnfRatAtlas2Median.expScores comma indexOf full hgFixed.gnfRatAtlas2MedianRatio.expScores comma indexOf full $rn.gnfAtlas2.expScores comma indexOf full identifier gnfU95SampleIdV0 "Identifiers of RNA samples used early version of GNF Human Expression Atlas 1" hgFixed.affyExps.id $hg.affyRatio.expIds comma $hg.affyRatio.expScores comma indexOf identifier gnfU95SampleIdV1 "Identifiers of RNA samples used in GNF Human Expression Atlas 1" hgFixed.gnfHumanU95AllExps.id hgFixed.gnfHumanU95All.expScores comma indexOf full hgFixed.gnfHumanU95AllRatio.expScores comma indexOf full identifier gnfU95MedianSampleIdV1 "Identifiers of pooled RNA samples used in GNF Human Expression Atlas 1" hgFixed.gnfHumanU95MedianExps.id hgFixed.gnfHumanU95Median.expScores comma indexOf full hgFixed.gnfHumanU95MedianRatio.expScores comma indexOf full identifier gnfU74aSampleId "Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74A Chip" hgFixed.gnfMouseU74aAllExps.id hgFixed.gnfMouseU74aAll.expScores comma indexOf full hgFixed.gnfMouseU74aAllRatio.expScores comma indexOf full $mm.affyGnfU74A.expIds comma full $mm.affyGnfU74A.expScores comma indexOf full identifier gnfU74aMedianSampleId "Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74A Chip" hgFixed.gnfMouseU74aMedianExps.id hgFixed.gnfMouseU74aMedian.expScores comma indexOf full hgFixed.gnfMouseU74aMedianRatio.expScores comma indexOf full identifier gnfU74bSampleId "Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74B Chip" hgFixed.gnfMouseU74bAllExps.id hgFixed.gnfMouseU74bAll.expScores comma indexOf full hgFixed.gnfMouseU74bAllRatio.expScores comma indexOf full $mm.affyGnfU74B.expIds comma full $mm.affyGnfU74B.expScores comma indexOf full identifier gnfU74bMedianSampleId "Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74B Chip" hgFixed.gnfMouseU74bMedianExps.id hgFixed.gnfMouseU74bMedian.expScores comma indexOf full hgFixed.gnfMouseU74bMedianRatio.expScores comma indexOf full identifier gnfU74cSampleId "Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74C Chip" hgFixed.gnfMouseU74cAllExps.id hgFixed.gnfMouseU74cAll.expScores comma indexOf full hgFixed.gnfMouseU74cAllRatio.expScores comma indexOf full $mm.affyGnfU74C.expIds comma full $mm.affyGnfU74C.expScores comma indexOf full identifier gnfU74cMedianSampleId "Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74C Chip" hgFixed.gnfMouseU74cMedianExps.id hgFixed.gnfMouseU74cMedian.expScores comma indexOf full hgFixed.gnfMouseU74cMedianRatio.expScores comma indexOf full identifier arbFlyLifeAllSampleId "Identifiers of RNA samples used in Arbeitman fly life cycle experiments" hgFixed.arbFlyLifeAllExps.id hgFixed.arbFlyLifeAll.expScores comma indexOf full hgFixed.arbFlyLifeAllRatio.expScores comma indexOf full identifier arbFlyLifeMedianSampleId "Identifiers of pooled RNA samples used in Arbeitman fly life cycle experiments" hgFixed.arbFlyLifeMedianExps.id hgFixed.arbFlyLifeMedian.expScores comma indexOf full hgFixed.arbFlyLifeMedianRatio.expScores comma indexOf full identifier kimWormLifeAllSampleId "Identifiers of RNA samples used in Kim worm life cycle experiments" hgFixed.kimWormLifeAllExps.id hgFixed.kimWormLifeAllRatio.expScores comma indexOf full identifier kimWormLifeMedianSampleId "Identifiers of pooled RNA samples used in Kim worm life cycle experiments" hgFixed.kimWormLifeMedianExps.id hgFixed.kimWormLifeMedianRatio.expScores comma indexOf full identifier yeastChoCellCycleSampleId "Identifiers of RNA samples used in Cho yeast cell cycle experiments" hgFixed.yeastChoCellCycleExps.id hgFixed.yeastChoCellCycle.expScores comma indexOf full hgFixed.yeastChoCellCycleRatio.expScores comma indexOf full identifier hgFixedSageExpId # I'd like to drop this table set. Check with Chuck. "Sage experiment (tissue type etc) ID in hgFixed" hgFixed.sageExp.num hgFixed.sage.exps comma full hgFixed.sageCounts.expCounts comma indexOf full identifier sageExpId "Sage experiment (tissue type etc) ID" $gbd.sageExp.num $gbd.sage.exps comma full identifier rinnSexSampleId "Identifiers of RNA samples used in Rinn Sex Experiments on mouse Affy MOE430 Chip" hgFixed.mouseRinnSexExps.id hgFixed.mouseRinnSex.expScores comma indexOf full hgFixed.mouseRinnSexRatio.expScores comma indexOf full identifier rinnSexMedianSampleId "Identifiers of median RNA samples used in Rinn Sex Experiments on mouse Affy MOE430 Chip" hgFixed.mouseRinnSexMedianExps.id hgFixed.mouseRinnSexMedian.expScores comma indexOf full hgFixed.mouseRinnSexMedianRatio.expScores comma indexOf full identifier stanfordPromotersCellId "Identifiers of cell lines for Stanford ENCODE project luciferase assays" hgFixed.encode_Stanford_PromotersExps.id $hg.encode_Stanford_Promoters.expIds comma full $hg.encode_Stanford_Promoters.expScores comma indexOf full identifier mouseLandscape "U. Toronto mouse gene probe ID" hgFixed.mouseLandscape.name $mm.knownToXM.value identifier mouseLandscapeSampleId "Identifiers of U. Toronto RNA samples" hgFixed.mouseLandscapeExps.id hgFixed.mouseLandscape.expScores comma indexOf full identifier gladHumESSampleId "Identifiers of RNA samples used in Gladstone Arrays" hgFixed.gladHumESExps.id hgFixed.gladHumES.expScores comma indexOf full hgFixed.gladHumESRatio.expScores comma indexOf full # Stuff to link together alignment chains and nets identifier chainSelf "Link together self chain info" $gbd.chainSelf.id $gbd.chainSelfLink.chainId full $oldSplit.chainSelf.id $split $oldSplit.chainSelfLink.chainId $split full $gbd.netSelf.chainId exclude=0 identifier chain[${chainDest}]Id "Link together chain info" $gbd.chain[].id $gbd.chain[]Link.chainId full $oldSplit.chain[].id $split $oldSplit.chain[]Link.chainId $split full $gbd.net[].chainId exclude=0 $gbd.netRxBest[].chainId exclude=0 $gbd.net[]NonGap.chainId exclude=0 $gbd.netSynteny[].chainId exclude=0 identifier chainRBest[${chainDest}]Id "Link together rbest chain info" $gbd.chainRBest[].id $gbd.chainRBest[]Link.chainId full $oldSplit.chainRBest[].id $split $oldSplit.chainRBest[]Link.chainId $split full $gbd.netRBest[].chainId exclude=0 identifier chainSyn[${chainDest}]Id "Link together rbest chain info" $gbd.chainSyn[].id $gbd.chainSyn[]Link.chainId full $oldSplit.chainSyn[].id $split $oldSplit.chainSyn[]Link.chainId $split full $gbd.netSyn[].chainId exclude=0 identifier rBestChainPanTro1Id "Link together reciprocal best chain/net" hg16.rBestChainPanTro1.id $split hg16.rBestChainPanTro1Link.chainId $split full hg16.rBestNetPanTro1.chainId exclude=0 # Sequences added using hgLoadSeq (seq+extFile) identifier seqExtFile "External sequences from various sources e.g. STS, fosEnds, microarray probes" $gbd.seq.acc identifier stsAccession external=genbank typeOf=seqExtFile "Genbank accession of a Sequence Tag Site (STS) sequence." $gbd.stsInfo2.genbank dupeOk identifier bacEndNames "Names for BAC end reads." $gbd.all_bacends.qName dupeOk $gbd.bacEndPairs.lfNames comma $danRer.bacEndSingles.lfNames comma $danRer.bacEndPairsBad.lfNames comma $danRer.bacEndAlias.alias minCheck=0.55 $hg.fishClones.beNames comma minCheck=0.70 identifier danRerBacExtName "External name for BAC clones." $danRer.bacCloneXRef.name dupeOk $danRer.bacEndPairs.name $danRer.bacEndSingles.name identifier danRerBacSangerName "Sanger's identifiers for BAC Clones" danRer3,danRer4.bacCloneXRef.sangerName dupeOk danRer3,danRer4.bacCloneAlias.sangerName minCheck=0.97 identifier bacAccession typeOf=seqExtFile external=genbank "Genbank accession of a sequenced BAC (~150kb of genomic sequence)." identifier humanBacAccession typeOf=bacAccession "Genbank accession of a sequenced $hg.BAC (~150kb of genomic sequence)." $hg.clonePos.name chopAfter=. dupeOk $hg,!hg16,!hg17,!hg18.gold.frag chopAfter=. $hgSplit,!hg18.gold.frag chopAfter=. $split hg18.gold.frag chopAfter=. $split minCheck=0.98 hg16.certificate.accession1 hg16.certificate.accession2 $hg,!hg16,!hg17,!hg18,!hg19.gl.frag chopAfter=. $hgSplit,hg19,!hg18.gl.frag chopAfter=. $split hg18.gl.frag chopAfter=. $split minCheck=0.95 $hg.fishClones.accNames chopAfter=. comma minCheck=0.70 identifier humanBacAccessionVersion typeOf=bacAccession "Genbank accession.version of sequence $hg.BAC" $hg.clonePos.name dupeOk $hg,!hg16,!hg17,!hg18.gl.frag chopAfter=_ $hgSplit,hg19,!hg18.gl.frag $split chopAfter=_ $hg,!hg16,!hg17,!hg18.gold.frag $hgSplit,!hg18.gold.frag $split hg18.gl.frag $split chopAfter=_ minCheck=0.95 hg18.gold.frag $split minCheck=0.90 identifier wgsContigAccession typeOf=seqExtFile "Genbank accession.version of whole-genome shotgun contig" $wgs.contigAcc.acc identifier wgsContigName "Sequencing project name for whole-genome shotgun contigs." $wgs.contigAcc.contig $wgs,!panTro1.gold.frag $split full set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9 identifier proteinAccession fuzzy "Genbank protein accession." $kgDb.kgProtAlias.alias $kgDb.kgSpAlias.alias minCheck=0.1 $kgDb.kgXref.protAcc hgFixed.refLink.protAcc identifier estOrMrnaAccession "Genbank EST or mRNA accession." hgFixed.gbSeq.acc hgFixed.gbCdnaInfo.acc unique hgFixed.imageClone.acc $gbd,!ce2,!hg16,!hg17,!hg18,!mm7.altGraphX.mrnaRefs comma ce2.altGraphX.mrnaRefs comma minCheck=0.96 hg16.altGraphX.mrnaRefs comma minCheck=0.99 hg17.altGraphX.mrnaRefs comma minCheck=0.97 hg18.altGraphX.mrnaRefs comma minCheck=0.98 mm7.altGraphX.mrnaRefs comma minCheck=0.99 identifier estAccession typeOf=estOrMrnaAccession "Genbank EST accession" identifier nativeEstAccession typeOf=estAccession "Genbank Native (same organism as database) EST accession" $gbd.all_est.qName dupeOk $gbd.est.qName full $gbd.intronEst.qName $oldSplit.est.qName $split full $oldSplit.intronEst.qName $split $gbd.estOrientInfo.name full identifier xenoEstAccession typeOf=estAccession "Genbank xeno (different organism from database) EST accession" $gbd.xenoEst.qName dupeOk identifier mrnaAccession typeOf=estOrMrnaAccession fuzzy "Genbank mRNA accession" identifier xenoMrnaAccession typeOf=mrnaAccession "Genbank xeno (different organism from database) mRNA accession" $gbd.xenoMrna.qName dupeOk identifier nativeMrnaAccession typeOf=mrnaAccession "Genbank Native (same organism as database) mRNA accession" $gbd.all_mrna.qName dupeOk $gbd,!ce2.mrnaOrientInfo.name full minCheck=0.01 ce2.mrnaOrientInfo.name minCheck=0.08 $gbd,!mm7,!mm8,!hg17,!hg18,!rn4.dupSpMrna.mrnaID minCheck=0.80 $gbd,!mm7,!mm8,!hg17,!hg18,!rn4.dupSpMrna.dupMrnaID minCheck=0.95 $gbd,!mm7,!mm8,!mm9,!mm10,!hg17,!rn3,!rn4.mrnaRefseq.mrna minCheck=0.25 mm7.mrnaRefseq.mrna minCheck=0.30 mm8.mrnaRefseq.mrna minCheck=0.30 mm9.mrnaRefseq.mrna minCheck=0.30 mm10.mrnaRefseq.mrna minCheck=0.30 hg17.mrnaRefseq.mrna minCheck=0.80 $rn.mrnaRefseq.mrna minCheck=0.03 $gbd,!hg17,!hg18,!hg19,!mm7,!mm8,!mm9,!mm10,!rn4,!hg38.spMrna.mrnaID minCheck=0.98 $mm.dupSpMrna.mrnaID minCheck=0.10 $mm.dupSpMrna.dupMrnaID minCheck=0.10 hg17.spMrna.mrnaID minCheck=0.30 hg17.dupSpMrna.mrnaID minCheck=0.20 hg17.dupSpMrna.dupMrnaID minCheck=0.20 hg18.dupSpMrna.mrnaID minCheck=0.20 hg18.dupSpMrna.dupMrnaID minCheck=0.70 identifier mgcAccession typeOf=nativeMrnaAccession "Mammalian Gene Collection Genbank mRNA accession." $gbd.mgcFullMrna.qName dupeOk $gbd.mgcGenes.name full identifier orfeomeAccession typeOf=nativeMrnaAccession "ORFeome collaboration Genbank mRNA accession." $gbd.orfeomeMrna.qName dupeOk $gbd.orfeomeGenes.name full identifier metaRefSeqId typeOf=mrnaAccession "RefSeq mRNA accession" hgFixed.refLink.mrnaAcc hgFixed.refSeqStatus.mrnaAcc $metaGbd.refFlat.name $metaGbd.refGene.name $metaGbd.refMrna.name $metaGbd.refSeqAli.qName hgFixed.refSeqSummary.mrnaAcc identifier refSeqId typeOf=mrnaAccession "RefSeq mRNA accession" hgFixed.refLink.mrnaAcc hgFixed.refSeqStatus.mrnaAcc minCheck=0.10 $kgDb.kgXref.refseq exclude= minCheck=0.50 $kgDb,!hg16,!hg17,!hg18,!mm7,!mm8,!mm9,!mm10.knownToRefSeq.value minCheck=0.98 hg18,mm7,mm8,mm9,mm10.knownToRefSeq.value minCheck=0.96 hg16,hg17.knownToRefSeq.value minCheck=0.93 $kgDb.refSeqKg.refseq minCheck=0.60 $ccdsDb,!hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.3 $gbd,!rn3.mrnaRefseq.refseq minCheck=0.25 rn3.mrnaRefseq.refseq minCheck=0.03 $gbd,!bosTau2,!bosTau3,!canFam1,!canFam2,!droSim1,!droYak1,!droYak2,!panTro1,!rheMac2,!dp2,!dp3.mrnaOrientInfo.name minCheck=0.0 # The rule above should only apply to mrnaOrientInfo entries from refSeq (not # the regular genBank mRNAs). The minCheck=0.0 preserves table relationshps. $gbd.refFlat.name $gbd.refGene.name $gbd.refMrna.name $gbd.refSeqAli.qName hgFixed.refSeqSummary.mrnaAcc minCheck=0.99 dm1.bdgpToRefSeq.value minCheck=0.9 $dm,!dm1.flyBaseToRefSeq.value minCheck=0.92 $mm.mrnaRefseq.mrna minCheck=0.03 $mm.dupSpMrna.mrnaID minCheck=0.60 $mm,!mm8,!mm9,!mm10.dupSpMrna.dupMrnaID minCheck=0.20 mm10.dupSpMrna.dupMrnaID minCheck=0.19 mm9.dupSpMrna.dupMrnaID minCheck=0.19 mm8.dupSpMrna.dupMrnaID minCheck=0.19 hg17.mrnaRefseq.mrna minCheck=0.10 hg17.spMrna.mrnaID minCheck=0.48 hg17.dupSpMrna.mrnaID minCheck=0.40 hg17.dupSpMrna.dupMrnaID minCheck=0.20 hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.37 $rn.rgdGene2ToRefSeq.value minCheck=0.95 identifier xenoRefSeqId typeOf=xenoMrnaAccession "Other Species RefSeq mRNA accession" $xrg.xenoRefGene.name dupeOk $xrg.xenoRefFlat.name full $xrg.xenoRefSeqAli.qName full identifier knownToRefSeqId typeOf=mrnaAccession "RefSeq mRNA accession in knownToRefSeq table" $kgDb.knownToRefSeq.value dupeOk mm7.geneNetworkId.id minCheck=0.80 mm8.geneNetworkId.id minCheck=0.80 mm9.geneNetworkId.id minCheck=0.40 mm10.geneNetworkId.id minCheck=0.40 hg19.geneNetworkId.id minCheck=0.40 rn3.geneNetworkId.id minCheck=0.40 identifier rgdGene2ToRefSeqId typeOf=mrnaAccession "RefSeq mRNA accession in rgdGene2ToRefSeq table" $kgDb.rgdGene2ToRefSeq.value dupeOk rn4.geneNetworkId.id minCheck=0.30 identifier kgOldId "Old Known Gene ID - the genbank accession of the representative mRNA" hg17.kgOld.name dupeOk hg17.kgXrefOld.kgId minCheck=.95 identifier rn4KgPrevious "rn4 knownGenePrevious was knownGene" rn4.knownGenePrevious.name dupeOk rn4.kgXrefPrevious.kgId identifier knownGeneId dependency "Known Gene ID - the genbank accession of the representative mRNA" $kgDb.knownGene.name dupeOk $kgDb.knownToRefSeq.name $kgDb.knownCanonToDecipher.name $kgDb.knownToDecipher.name $kgDb.knownToKeggEntrez.name hg16.hg17Kg.name minCheck=.30 $kgDb2.knownExpDistance.query $kgDb2.knownExpDistance.target $kgDb.bioCycPathway.kgID $kgDb.ceBlastTab.query $kgDb.hgBlastTab.query $kgDb.dmBlastTab.query $kgDb.drBlastTab.query $kgDb.mmBlastTab.query $kgDb.rnBlastTab.query $kgDb.scBlastTab.query $kgDb,!rn3.dupSpMrna.mrnaID rn3.dupSpMrna.mrnaID minCheck=0.90 $kgDb.foldUtr3.name $kgDb.foldUtr5.name $hg.gnfU95Distance.query $hg.gnfU95Distance.target $kgDb.gnfAtlas2Distance.query $kgDb.gnfAtlas2Distance.target $kgDb.affyGnfU74ADistance.query $kgDb.affyGnfU74ADistance.target $kgDb.affyGnfU74BDistance.query $kgDb.affyGnfU74BDistance.target $kgDb.affyGnfU74CDistance.query $kgDb.affyGnfU74CDistance.target $kgDb.mouseLandscapeDistance.query minCheck=0.94 $kgDb.mouseLandscapeDistance.target minCheck=0.94 $hg.gladHumESDistance.query $hg.gladHumESDistance.target $kgDb.kgAlias.kgID $kgDb.kgProtAlias.kgID $kgDb.kgSpAlias.kgID $kgDb.kgXref.kgID full $kgDb.kgTxInfo.name full $kgDb.knownBlastTab.query $kgDb.knownBlastTab.target $kgDb.knownCanonical.transcript $kgDb.knownGeneMrna.name full $kgDb,!hg18,!mm9,!mm10.knownGeneLink.name $kgDb.knownIsoforms.transcript full $kgDb.knownToAllenBrain.name $kgDb.knownToCdsSnp.name $kgDb.knownToEnsembl.name $kgDb.knownToLynx.name $kgDb.ucscScop.ucscId $kgDb.knownToMrna.name $kgDb.knownToMrnaSingle.name $kgDb.knownToNextProt.name $kgDb.knownToGnf1h.name $kgDb.knownToGnfAtlas2.name $kgDb.knownToHInv.name $kgDb.knownToHprd.name $kgDb.knownToLocusLink.name $kgDb.knownToPfam.name $kgDb.knownToMupit.name $kgDb.knownToSuper.gene $kgDb.knownToTag.name $kgDb.knownToTreefam.name $kgDb.knownToU133.name $kgDb.knownToU133Plus2.name $kgDb.knownToU95.name $kgDb.knownToVisiGene.name $kgDb.knownToWikipedia.name $kgDb.refSeqKg.kgId minCheck=0.50 $kgDb.rankProp.query $kgDb.rankProp.target $kgDb.pPsiBlast.kgId1 $kgDb.pPsiBlast.kgId2 $ccdsDb.ccdsKgMap.geneId $kgDb2,!rn4.knownGenePep.name full $kgDb3.knownGenePep.name $kgDb3,!hg38,!mm10.knownCanonical.protein exclude= $kgDb3.kgProtMap2.qName $kgDb.keggPathway.kgID $hg.humanHprdP2P.query $hg.humanHprdP2P.target $hg.humanVidalP2P.query $hg.humanVidalP2P.target $hg.humanWankerP2P.query $hg.humanWankerP2P.target $kgDb.kgColor.kgID full $kgDb.kg2ToKg3.newId minCheck=0.5 exclude= $kgDb.kg3ToKg4.oldId minCheck=0.5 exclude= $kgDb.kg3ToKg4.newId minCheck=0.5 exclude= $kgDb,!hg19.kg4ToKg5.newId minCheck=0.5 exclude= $kgDb,!mm10.kg5ToKg6.newId exclude= $kgDb,!mm10.kg6ToKg7.newId exclude= $kgDb,!mm10.kg7ToKg8.newId exclude= $kgDb,!mm10.kg8ToKg9.newId exclude= $kgDb,!hg38,!mm10.kg9ToKg10.newId exclude= $kgDb.kg10ToKg11.newId exclude= $kgDb,!hg16.kgTargetAli.qName full hg19.knownGeneTxMrna.name hg19.knownGeneTxPep.name $kgDb.kg11ToKg12.newId exclude= $kgDb.knownAttrs.kgID $kgDb.knownCds.name identifier knownGeneOld11Id dependency "Previous UCSC Gene build" $kgDb.knownGeneOld11.name $kgDb.kg10ToKg11.oldId full $kgDb.kgXrefOld11.kgID full identifier knownGeneOld10Id dependency "Previous UCSC Gene build" $kgDb.knownGeneOld10.name $kgDb.kg10ToKg11.oldId full $kgDb.kgXrefOld10.kgID full identifier knownGeneOld9Id dependency "Previous UCSC Gene build" $kgDb.knownGeneOld9.name $kgDb.kg9ToKg10.oldId full $kgDb.kgXrefOld9.kgID full identifier knownGeneOld8Id dependency "Previous UCSC Gene build" $kgDb.knownGeneOld8.name $kgDb.kg8ToKg9.oldId full $kgDb.kgXrefOld8.kgID full identifier knownGeneOld7Id dependency "Previous UCSC Gene build" $kgDb.knownGeneOld7.name $kgDb.kg7ToKg8.oldId full $kgDb.kgXrefOld7.kgID full identifier knownGeneOld6Id dependency "Previous UCSC Gene build" $kgDb.knownGeneOld6.name $kgDb.kg6ToKg7.oldId full $kgDb.kgXrefOld6.kgID full identifier knownGeneOld5Id dependency "Previous UCSC Gene build" $kgDb,!mm10.knownGeneOld5.name $kgDb.kg5ToKg6.oldId full $kgDb.kgXrefOld5.kgID full identifier knownGeneOldId dependency "Still-previous UCSC Genes build" $kgDb,!hg19.knownGeneOld4.name $kgDb,!hg19.kg4ToKg5.oldId full identifier knownGeneOld3Id dependency "Still-still previous UCSC Genes build" $kgDb.knownGeneOld3.name $kgDb.kg3ToKg4.oldId full identifier knownGeneOld2Id dependency "Old knownGene (KGII) and kgXref tables kept after KGIII implementation - still needed?" $kgDb.knownGeneOld2.name dupeOk $kgDb.kgXrefOld2.kgID full $kgDb.humanBlastTab.query $kgDb.humanBlastTab.target identifier knownToHprdName "Dependencies on knownToHprd.name" $kgDb.knownToHprd.name dupeOk $kgDb.humanHprdP2P.target identifier pfamDesc "pfam description for each accession" $kgDb.pfamDesc.pfamAC $kgDb.knownToPfam.value identifier scopName "scop Domain Names" $kgDb.ucscScop.domainName dupeOk $kgDb.scopDesc.name full minCheck=0.60 identifier scopToUcscId "scop Domains to UCSC Id" $kgDb.kgProtMap2.qName $kgDb,!hg18.ucscScop.ucscId minCheck=0.99 hg18.ucscScop.ucscId minCheck=0.70 identifier knownIsoformCluster "ID of a cluster of overlapping known genes" $kgDb.knownCanonical.clusterId $kgDb.knownIsoforms.clusterId full identifier rgdGene2IsoformCluster "ID of a cluster of overlapping rgdGene2 genes" $kgDb.rgdGene2Canonical.clusterId $kgDb.rgdGene2Isoforms.clusterId full # known relationship for both KG2 and KG3, but doesn't work across dbs. identifier knownXref "Swissprot IDs" $hg.kgXref.spID dupeOk proteome.spXref2.accession proteome.hgncXref.uniProt identifier ccdsGeneId "CCDS Gene ID" $ccdsDb.ccdsGene.name dupeOk $ccdsDb.ccdsInfo.ccds full $ccdsDb.ccdsKgMap.ccdsId $ccdsDb.ccdsNotes.ccds identifier ctdGeneSymbol "CTD Gene Symbol" hgFixed.ctdSorted.GeneSymbol dupeOk $hg.kgXref.geneSymbol minCheck=0.30 identifier rdmrGene "R-DMR Gene" $hg.rdmr.name dupeOk $hg.rdmrRaw.gene minCheck=0.95 identifier gadId "GAD Gene ID" $hg.kgXref.geneSymbol dupeOk $hg.gad.name minCheck=0.94 identifier gadAllId "GAD Gene Symbol in raw input" $hg.kgXref.geneSymbol dupeOk $hg.gadAll.geneSymbol minCheck=0.95 identifier hugeId "HuGE Gene ID" $hg.kgXref.geneSymbol dupeOk $hg.huge.geneSymbol minCheck=0.89 # Fields parsed out of a Genbank flat file, associated with mRNA records identifier metaGbCdnas "Connect metaGbd gbCdnaInfo with mRNA/EST" hgFixed.gbCdnaInfo.acc $metaGbd.all_mrna.qName $metaGbd.all_est.qName $metaGbd.refGene.name $metaGbd.xenoRefGene.name hgFixed.gbMiscDiff.acc $metaGbd.refSeqAli.qName $metaGbd.xenoRefSeqAli.qName $metaGbd.xenoMrna.qName $metaGbd.xenoEst.qName hgFixed.gbWarn.acc identifier gbCdnas "Connects gbCdnaInfo with mRNA/EST" hgFixed.gbCdnaInfo.acc $gbd.all_mrna.qName $gbd.all_est.qName $gbd.refGene.name $gbd.xenoRefGene.name hgFixed.gbMiscDiff.acc $gbd.refSeqAli.qName $gbd.xenoRefSeqAli.qName $gbd.xenoMrna.qName $gbd.xenoEst.qName hgFixed.gbWarn.acc identifier metaGenBankAuthor "Connects metaGenBank mRNA/EST and its author" hgFixed.author.id hgFixed.gbCdnaInfo.author identifier metaGenBankCds "Connects metaGenBank mRNA/EST and its coding region (CDS)" hgFixed.cds.id hgFixed.gbCdnaInfo.cds identifier metaGenBankCell "Connects metaGenBank mRNA/EST and the cell type it came from" hgFixed.cell.id hgFixed.gbCdnaInfo.cell identifier metaGenBankDevelopment "Connects metaGenBank mRNA/EST and development stage of the organism it came from" hgFixed.development.id hgFixed.gbCdnaInfo.development identifier metaGenBankDescription "Connects metaGenBank mRNA/EST and descriptive text" hgFixed.description.id hgFixed.gbCdnaInfo.description identifier metaGenBankGeneName "Connects metaGenBank mRNA/EST and gene name" hgFixed.geneName.id hgFixed.gbCdnaInfo.geneName hgFixed.refLink.geneName identifier metaGenBankKeyword "Connects metaGenBank mRNA/EST and keyword" hgFixed.keyword.id hgFixed.gbCdnaInfo.keyword identifier metaGenBankLibrary "Connects metaGenBank mRNA/EST and cDNA library" hgFixed.library.id hgFixed.gbCdnaInfo.library identifier metaGenBankMrnaClone "Connects metaGenBank mRNA/EST and cDNA clone name" hgFixed.mrnaClone.id hgFixed.gbCdnaInfo.mrnaClone identifier metaGenBankOrganism "Connects metaGenBank mRNA/EST and organism it came from" hgFixed.organism.id hgFixed.gbCdnaInfo.organism identifier metaGenBankProductName "Connects metaGenBank mRNA/EST and protein product name" hgFixed.productName.id hgFixed.gbCdnaInfo.productName hgFixed.refLink.prodName identifier metaGenBankSex "Connects metaGenBank mRNA/EST and sex mRNA came from" hgFixed.sex.id hgFixed.gbCdnaInfo.sex identifier metaGenBankSource "Connects metaGenBank mRNA/EST and source of mRNA" hgFixed.source.id hgFixed.gbCdnaInfo.source identifier metaGenBankTissue "Connects metaGenBank mRNA/EST and tissue mRNA isolated from" hgFixed.tissue.id hgFixed.gbCdnaInfo.tissue identifier genBankAuthor "Connects genBank mRNA/EST and its author" hgFixed.author.id hgFixed.gbCdnaInfo.author identifier genBankCds "Connects genBank mRNA/EST and its coding region (CDS)" hgFixed.cds.id hgFixed.gbCdnaInfo.cds identifier genBankCell "Connects genBank mRNA/EST and the cell type it came from" hgFixed.cell.id hgFixed.gbCdnaInfo.cell identifier genBankDevelopment "Connects genBank mRNA/EST and development stage of the organism it came from" hgFixed.development.id hgFixed.gbCdnaInfo.development identifier genBankDescription "Connects genBank mRNA/EST and descriptive text" hgFixed.description.id hgFixed.gbCdnaInfo.description identifier genBankGeneName "Connects genBank mRNA/EST and gene name" hgFixed.geneName.id hgFixed.gbCdnaInfo.geneName hgFixed.refLink.geneName identifier genBankKeyword "Connects genBank mRNA/EST and keyword" hgFixed.keyword.id hgFixed.gbCdnaInfo.keyword identifier genBankLibrary "Connects genBank mRNA/EST and cDNA library" hgFixed.library.id hgFixed.gbCdnaInfo.library $gbd,!hg17.altGraphX.mrnaLibs comma hg17.altGraphX.mrnaLibs comma minCheck=0.99 identifier genBankMrnaClone "Connects genBank mRNA/EST and cDNA clone name" hgFixed.mrnaClone.id hgFixed.gbCdnaInfo.mrnaClone identifier genBankOrganism "Connects genBank mRNA/EST and organism it came from" hgFixed.organism.id hgFixed.gbCdnaInfo.organism identifier genBankProductName "Connects genBank mRNA/EST and protein product name" hgFixed.productName.id hgFixed.gbCdnaInfo.productName hgFixed.refLink.prodName identifier genBankSex "Connects genBank mRNA/EST and sex mRNA came from" hgFixed.sex.id hgFixed.gbCdnaInfo.sex identifier genBankSource "Connects genBank mRNA/EST and source of mRNA" hgFixed.source.id hgFixed.gbCdnaInfo.source identifier genBankTissue "Connects genBank mRNA/EST and tissue mRNA isolated from" hgFixed.tissue.id hgFixed.gbCdnaInfo.tissue $gbd.altGraphX.mrnaTissues comma # Some misc clone-oriented identifiers identifier bacCloneName fuzzy "A Roswell Park, Cal Tech or other clone ID" $gbd.fishClones.name $gbd.bacEndPairs.name identifier imageCloneId external=IMAGEConsortium fuzzy "An image cDNA clone ID" hgFixed.imageClone.imageId identifier humanFosmidId "Human Fosmid (~50kb genomic sequence) clone" $hg.fosEndPairs.name dupeOk identifier humanFosmidEndId "Identifier of read from one end of human formid." $hg.all_fosends.qName dupeOk $hg.fosEndPairs.lfNames comma ## TYPED TO HERE %%% # Mapping Stuff, STS, etc. set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9 identifier dbStsId external=dbSts fuzzy "NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID" $hg.all_sts_primer.qName chopBefore=dbSTS_ $gbd,$notDbStsId.all_sts_seq.qName $gbd,$notDbStsId.stsInfo2.dbSTSid identifier ucscStsId "UCSC STS (Sequenced Tagged Site, aka mapping sequence) ID" $gbd.stsInfo2.identNo $gbd.stsAlias.identNo $gbd.stsMap.identNo identifier ucscMouseStsId "UCSC Mouse STS (Sequenced Tagged Site, aka mapping sequence) ID" $mm.stsInfoMouseNew.identNo $mm.stsAlias.identNo $mm.all_sts_primer.qName chopAfter=_ minCheck=0.99 $mm.stsMapMouseNew.identNo set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9 identifier stsName fuzzy "STS (Sequenced Tagged Site, aka mapping sequence) Name" $hg.fishClones.stsNames comma $gbd,$notStsName.stsInfo2.otherNames comma $mm.stsInfoMouseNew.alias separator=; identifier stsTrueName typeOf=stsName "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name" $gbd,!hg16.stsInfo2.name $gbd.stsAlias.trueName $gbd.stsMap.name identifier stsTrueNameHg16 typeOf=stsName "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name for hg16" hg16.stsInfo2.name dupeOk hg16.stsAlias.trueName hg16.stsMap.name identifier mouseStsTrueName typeOf=stsName "Mouse STS (Sequenced Tagged Site, aka mapping sequence) Unique Name" $mm.stsInfoMouseNew.name $mm.stsAlias.trueName minCheck=0.99 $mm,!mm7,!mm8,!mm9,!mm10.all_sts_primer.qName chopBefore=_ minCheck=0.99 mm7,mm8,mm9,mm10.all_sts_primer.qName chopBefore=_ minCheck=0.98 $mm.stsMapMouseNew.name $mm.jaxQTL3.marker exclude= minCheck=0.99 $mm.jaxQTL3.flank1 exclude= minCheck=0.95 $mm.jaxQTL3.flank2 exclude= minCheck=0.99 identifier ratStsTrueName typeOf=stsName "Rat STS (Sequenced Tagged Site, aka mapping sequence) Unique Name" $rn.stsInfoRat.name dupeOk $rn,!rn3.stsMapRat.name rn3.stsMapRat.name minCheck=0.99 identifier rhMapName "Zebrafish RH (Radiation Hybrid) Map Name" $danRer.rhMap.qName dupeOk $danRer.rhMapZfishInfo.name minCheck=0.90 unique identifier igtcName "IGTC (genetrap.org) sequence name" $mm.seq.acc $mm.igtc.qName identifier kompName "KOMP (knockoutmouse.org) gene name" $mm.komp.name dupeOk $mm.kompExtra.name identifier ikmcName "IKMC (knockoutmouse.org) gene name" $mm.ikmc.name dupeOk $mm.ikmcExtra.name minCheck=0.99 identifier hgIkmcName "IKMC (knockoutmouse.org) mapped gene name" $hg.hgIkmc.name dupeOk $hg.hgIkmcExtra.name minCheck=0.99 # "Biological" Gene Names identifier metaHugoName external=HUGO fuzzy "International Human Gene Identifier" hgFixed.refLink.name $metaGbd.refFlat.geneName identifier hugoName external=HUGO fuzzy "International Human Gene Identifier" hgFixed.refLink.name $hg.atlasOncoGene.locusSymbol $hg.kgAlias.alias $hg.kgSpAlias.alias minCheck=0.1 $hg.kgXref.geneSymbol $hg.refFlat.geneName $hg.jaxOrtholog.humanSymbol $hg.omimMorbidMap.geneSymbols visiGene.gene.name $rn,!rn5.rgdGeneXref3.geneSymbol identifier kgGeneSymbol "UCSC Genes Gene Symbol" $hg.kgXref.geneSymbol dupeOk $hg.omimGeneMap.geneSymbol comma minCheck=0.37 $hg.omimGeneMap2.geneSymbol comma minCheck=0.37 $hg.omimMorbidMap.geneSymbols comma minCheck=0.25 hgFixed.ggLink.gene1 minCheck=0.8 hgFixed.ggLink.gene2 minCheck=0.8 hgFixed.ggGeneClass.gene minCheck=0.8 hgFixed.ggGeneName.gene minCheck=0.6 identifier mouseGeneName fuzzy "Mouse gene name from Jackson Labs/RefSeq" $hg.jaxOrtholog.mouseSymbol hgFixed.refLink.name visiGene.gene.name # Model Organism Database Identifiers identifier jaxMgiId "Jackson Labs Mouse Gene Identifier" $hg.jaxOrtholog.mgiId identifier wormBaseIsoformCluster "Overlapping (after splicing) WormBase transcripts" $ce.sangerCanonical.clusterId $ce.sangerIsoforms.clusterId full set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9 identifier wormBaseId external=WormBase dependency "WormBase (C. elegans) ORF ID" $ce.sangerGene.name $gbd,$notWormBaseId.ceBlastTab.target minCheck=0.90 $ce.kimExpDistance.query minCheck=0.68 $ce.kimExpDistance.target minCheck=0.66 $ce.orfToGene.name $ce.sangerBlastTab.query $ce.sangerBlastTab.target $ce.sangerCanonical.transcript $ce.sangerIsoforms.transcript $ce.sangerLinks.orfName minCheck=0.96 $ce.sangerPep.name minCheck=0.96 $ce.sangerToKim.name $ce.sangerToPfam.name $ce.sangerToRefSeq.name $ce.dmBlastTab.query $ce,!ce2.drBlastTab.query $ce.hgBlastTab.query $ce,!ce2.mmBlastTab.query $ce,!ce2.rnBlastTab.query $ce.scBlastTab.query $ce.sangerGeneToWBGeneID.sangerGene identifier wormBasePseudoGene external=WormBase dependency "WormBase (C. elegans) pseudo genes" $ce.sangerPseudoGene.name identifier wormBaseRnaGene external=WormBase dependency "WormBase (C. elegans) RNA genes" $ce.sangerRnaGene.name identifier flyBaseRefId "FlyBase (Drosophila) Reference (Literature)" $dm.fbRef.id $dm.fbPhenotype.fbRef identifier flyBaseAlleleId "FlyBase (Drosophila) Allele ID" $dm.fbAllele.id $dm.fbPhenotype.fbAllele exclude=0 set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9 identifier flyBaseGeneId external=FlyBase "FlyBase (Drosophila) Gene ID" $dm.fbGene.geneId $dm.bdgpExprLink.flyBaseId minCheck=0.95 dm1.bdgpGeneInfo.flyBaseId minCheck=0.95 dm1.bdgpNonCodingInfo.flyBaseId minCheck=0.20 dm1.bdgpSwissProt.flyBaseId minCheck=0.95 $dm.fbAllele.geneId $dm.fbPhenotype.geneId $dm.fbSynonym.geneId $dm.fbTranscript.geneId minCheck=0.95 dm1.flyBaseSwissProt.flyBaseId minCheck=0.95 $dm,!dm1.flyBase2004Xref.fbgn minCheck=0.90 $dm,!dm1.pscreen.geneIds comma minCheck=0.95 $gbd,$notFlyBaseGeneId.dmBlastTab.target minCheck=0.90 identifier bdgpIsoformCluster "Overlapping (after splicing) BDGP Drosophila transcripts" dm1.bdgpCanonical.clusterId dm1.bdgpIsoforms.clusterId full identifier bdgpGeneId external=BDGP "Berkeley Drosophila Genome Project Gene ID" dm1.bdgpGeneInfo.bdgpName dm1.bdgpExprLink.bdgpName minCheck=0.85 dm1.bdgpToCanonical.value identifier bdgpTranscriptId external=BDGP dependency "Berkeley Drosophila Genome Project Transcript ID" dm1.bdgpGene.name dm1.arbExpDistance.query dm1.arbExpDistance.target dm1.bdgpBlastTab.query dm1.bdgpBlastTab.target dm1.bdgpCanonical.transcript dm1.bdgpIsoforms.transcript dm1.bdgpGenePep.name dm1.bdgpSwissProt.bdgpName dm1.bdgpToCanonical.name dm1.bdgpToLocusLink.name minCheck=0.80 dm1.bdgpToPfam.name dm1.bdgpToRefSeq.name minCheck=0.97 dm1.ceBlastTab.query dm1.drBlastTab.query dm1.hgBlastTab.query dm1.mmBlastTab.query dm1.rnBlastTab.query dm1.scBlastTab.query dm1.fbTranscript.transcriptId minCheck=0.95 dm1.hgBlastTab.query dm1.blastFBPep00.name dm1.pscreen.geneIds comma minCheck=0.90 identifier bdgpNonCodingId external=BDGP "Berkeley Drosophila Genome Project Noncoding Gene ID" dm1.bdgpNonCoding.name chopAfter=- dupeOk dm1.bdgpNonCodingInfo.bdgpName minCheck=0.89 set flyBase2004IdDmDb ce2,ce4,danRer3,hg17,hg18,hg19,mm7,mm8,mm9,rn3,rn4,sacCer1,sacCer2,sacCer3 identifier flyBase2004IdDm external=FlyBase "FlyBase Xref as of 2004 for dm" $dm.flyBase2004Xref.name $dm,!dm1.flyBaseGene.name minCheck=0.99 $dm,!dm1.flyBasePep.name $dm,!dm1.flyBaseNoncoding.name minCheck=0.90 $dm,!dm1.arbExpDistance.query $dm,!dm1.arbExpDistance.target $dm,!dm1.ceBlastTab.query $dm,!dm1.drBlastTab.query minCheck=0.97 $dm,!dm1.hgBlastTab.query minCheck=0.96 $dm,!dm1.mmBlastTab.query minCheck=0.99 $dm,!dm1.rnBlastTab.query $dm,!dm1.scBlastTab.query $dm,!dm1.flyBaseBlastTab.query $dm,!dm1.flyBaseBlastTab.target $dm,!dm1.flyBaseCanonical.transcript $dm,!dm1.flyBaseIsoforms.transcript $dm,!dm1.flyBaseToRefSeq.name $dm,!dm1.flyBaseToUniProt.name $dm,!dm1.flyBaseToPfam.name $dm,!dm1.flyBaseToCG.name $dm,!dm1.flyBaseToDescription.name $dm,!dm1.flyP2P.query minCheck=0.98 $dm,!dm1.flyP2P.target minCheck=0.98 $flyBase2004IdDmDb.dmBlastTab.target minCheck=0.90 identifier flyBaseRelease6 external=FlyBase "FlyBase genes Release 6 for dm6" dm6.flyBaseGene.name dm6.flyBaseGenePep.name minCheck=0.99 identifier flyBase2004IdDp external=FlyBase "FlyBase Xref as of 2004 for dp3" dp3.flyBase2004Xref.name dp3.flyBaseGene.name identifier flyregId external=FlyReg "FlyReg motif name" $dm.flyregMotif.name $dm.flyreg.name minCheck=0.8 $dm.flyreg2.name minCheck=0.8 identifier sgdIsoformCluster "Overlapping (after splicing) SGD (Yeast) transcripts" $sacCer.sgdCanonical.clusterId $sacCer.sgdIsoforms.clusterId full identifier sgdProtHomologId "sacCer protHomolog protein ID" $sacCer.protHomolog.proteinID dupeOk $sacCer.samSubdir.proteinId identifier sgdId external=SGD "Sacchromyces Genome Database ID - Coding or other" set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9 identifier sgdCodingId typeOf=sgdId dependency "Sacchromyces Genome Database ID" $sacCer.sgdGene.name $gbd,$notSgdCodingId.scBlastTab.target minCheck=0.90 $sacCer.sgdBlastTab.query $sacCer.sgdBlastTab.target $sacCer.ceBlastTab.query $sacCer.dmBlastTab.query $sacCer,!sacCer1.drBlastTab.query $sacCer.hgBlastTab.query minCheck=0.999 $sacCer.mmBlastTab.query $sacCer.rnBlastTab.query sacCer2.knownBlastTab.query $sacCer.choExpDistance.target minCheck=0.60 $sacCer.choExpDistance.query minCheck=0.60 $sacCer.sgdCanonical.transcript $sacCer.sgdDescription.name $sacCer.sgdIsoforms.transcript $sacCer.sgdAbundance.name minCheck=0.95 $sacCer.sgdLocalization.name minCheck=0.95 $sacCer.sgdPep.name $sacCer.sgdToSwissProt.name minCheck=0.85 $sacCer.sgdToName.name minCheck=0.86 $sacCer.esRegGeneToModule.gene minCheck=0.94 $sacCer.esRegGeneToMotif.gene minCheck=0.97 $sacCer.esRegUpstreamRegion.name minCheck=0.96 $sacCer.sgdToPfam.name minCheck=0.55 identifier sgdNoncodingId typeOf=sgdId "Sacchromyces Genome Database Noncoding/Dubious feature ID" $sacCer.sgdOther.name dupeOk $sacCer.sgdOtherDescription.name # RGD Family Identifiers identifier rgdGeneId external=RGD "RGD gene ID" $rn.rgdGeneLink.refSeq $rn.rgdGene.name identifier rgdEstId external=RGD "RGD EST ID" $rn.rgdEstLink.name $rn.rgdEst.qName identifier rgdQtlId external=RGD "RGD QTL ID" $rn,$hg.rgdQtl.name $hg.rgdQtlLink.name minCheck=0.88 $rn.rgdQtlLink.name minCheck=0.99 identifier rgdRatQtlId external=RGD "RGD Rat QTL ID mapped to other organism" $hg.rgdRatQtl.name dupeOk $hg.rgdRatQtlLink.name minCheck=0.89 identifier rgdSslpId external=RGD "RGD SSLP ID" $rn.rgdSslp.name $rn.rgdSslpLink.name # New RGD Genes Family Identifiers identifier rgdGene2IdRaw external=RGD "Raw RGD Genes ID" $rn.rgdGene2.name chopBefore=RGD: $rn.genes_rat.gene_rgd_id minCheck=0.40 identifier rgdGene2Id external=RGD "RGD Genes ID" $rn.rgdGene2.name $rn.rgdGenePathway.geneId minCheck=0.75 $rn.rgdGene2BlastTab.query minCheck=0.75 $rn.rgdGene2BlastTab.target minCheck=0.75 $rn.scBlastTab.query minCheck=0.75 $rn.mmBlastTab.query minCheck=0.75 $rn.hgBlastTab.query minCheck=0.75 $rn.dmBlastTab.query minCheck=0.75 $rn.drBlastTab.query minCheck=0.75 $rn.ceBlastTab.query minCheck=0.75 $rn.rgdGene2ToDisplayId.name minCheck=0.75 $rn.rgdGene2ToUniProt.name minCheck=0.75 $rn.rgdGene2ToPDB.name minCheck=0.75 $rn.rgdGene2ToPfam.name minCheck=0.75 $rn.rgdGene2Xref.rgdGeneId minCheck=0.75 $rn.rgdGene2Pep.name minCheck=0.75 $rn.rgdGene2ToDescription.name minCheck=0.65 $rn.rgdGene2Pep.name minCheck=0.75 $rn.rgdGene2ToSymbol.rgdId minCheck=.75 $rn.rgdGene2ToU34A.name minCheck=.75 $rn.rgdGene2ToSuper.name minCheck=.75 $rn.rgdGene2ToRAE230.name minCheck=.75 $rn.rgdGene2ToRefSeq.name minCheck=.75 $rn.rgdGene2ToLocusLink.name minCheck=.75 $rn.rgdGene2ToGnfAtlas2.name minCheck=.75 $rn.rgdGene2ToKeggEntrez.name minCheck=.75 $rn.rgdGene2ToGenbankAll.name minCheck=.75 $rn.rgdGene2ToGenbank.name minCheck=.75 $rn.rgdGene2ToEnsembl.name minCheck=.75 $rn.rgdGene2ToCdsSnp.name minCheck=.75 $rn.affyExonTissuesGsMedianDistRgdGene2.query minCheck=.75 $rn.affyExonTissuesGsMedianDistRgdGene2.target minCheck=.75 $rn.affyExonTissuesGsMedianRgdGene2.name minCheck=.75 $rn.affyExonTissuesGsRgdGene2.name minCheck=.75 $rn.gnfAtlas2RgdGene2Distance.query minCheck=.75 $rn.gnfAtlas2RgdGene2Distance.target minCheck=.75 $rn.rgdGene2Canonical.transcript minCheck=.75 $rn.rgdGene2Isoforms.transcript minCheck=.75 $rn.rgdGene2KeggPathway.rgdId minCheck=.75 identifier rgdPathwayId external=RGD "RGD Pathway ID" $rn.rgdPathway.pathwayId $rn.rgdGenePathway.pathwayId minCheck=.90 # The Ensembl Gmish identifier ensemblGeneId external=Ensembl "Ensemble Gene ID" $gbd.ensTranscript.gene_name dupeOk $gbd.ensGtp.gene chopAfter=. $gbd.ensGeneXref.gene_name identifier ensemblGeneId3 external=Ensembl "Ensemble Gene ID" $gbd.ensemblXref3.gene dupeOk identifier ensemblProteinId external=Ensembl "Ensemble Translated Protein ID" $gbd.ensTranscript.translation_name dupeOk $gbd.ensGtp.protein chopAfter=. $gbd.sfAssign.seqID minCheck=0.01 identifier ensemblProteinId3 external=Ensembl "Ensemble Translated Protein ID" $gbd.ensemblXref3.protein dupeOk $gbd.sfAssign.seqID minCheck=0.01 set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!xenLae2,!xenTro7,!xenTro9 identifier ensemblTranscriptId external=Ensembl dependency "Ensembl Transcript ID" $ensGeneDb,$notEnsemblTranscriptId.ensGene.name dupeOk $gbd,$notEnsemblTranscriptId.ensGeneXref.transcript_name minCheck=0.95 $ensGeneDb,$notEnsemblTranscriptId.ensGtp.transcript minCheck=0.94 $ensGeneDb,$notEnsemblTranscriptId.ensPep.name minCheck=0.93 $gbd,$notEnsemblTranscriptId.ensTranscript.transcript_name minCheck=0.20 $gbd,$notEnsemblTranscriptId.ensInfo.name minCheck=0.9 $ensGeneDb,$notEnsemblTranscriptId.ensemblToGeneName.name minCheck=0.94 $ensGeneDb,$notEnsemblTranscriptId.ensemblSource.name minCheck=0.96 !hg38,$kgDb.knownToEnsembl.value chopAfter=. $kgDb.rgdGene2ToEnsembl.value chopAfter=. $danRer.ensZfishBlastTab.query $danRer.ensZfishBlastTab.target $danRer.ceBlastTab.query $danRer.dmBlastTab.query $danRer.hgBlastTab.query $danRer.mmBlastTab.query $danRer.rnBlastTab.query $danRer.scBlastTab.query rn6.ensToRgd.name minCheck=0.01 identifier obsoleteEnsemblTranscriptId external=Ensembl dependency "Ensembl Transcript ID" $obsoleteEnsGeneDb,$notEnsemblTranscriptId.ensGene.name chopAfter=. dupeOk $obsoleteEnsGeneDb,$notEnsemblTranscriptId.ensGtp.transcript chopAfter=. minCheck=0.94 $obsoleteEnsGeneDb,$notEnsemblTranscriptId.ensPep.name chopAfter=. minCheck=0.93 $obsoleteEnsGeneDb,$notEnsemblTranscriptId.ensemblToGeneName.name minCheck=0.96 $obsoleteEnsGeneDb,$notEnsemblTranscriptId.ensemblSource.name minCheck=0.96 identifier ensemblTranscriptWGS external=Ensembl dependency "Ensembl Transcript ID for WGS assemblies" $ensGeneWgs.ensGene.name dupeOk $ensGeneWgs.ensGtp.transcript minCheck=0.99 $ensGeneWgs.ensPep.name minCheck=0.99 $ensGeneWgs.ensInfo.name minCheck=0.99 $ensGeneWgs.ensemblToGeneName.name minCheck=0.99 $ensGeneWgs.ensemblSource.name minCheck=0.99 identifier ensemblGeneScaffold external=Ensembl dependency "Ensembl gene scaffold table chrom names" $ensGeneScaffold.chromInfo.chrom $ensGeneScaffold.ensemblGeneScaffold.chrom identifier altSeqLiftOver "alternate sequence lift over" hg38.chromInfo.chrom hg38.altSeqLiftOverPsl.qName hg38.altSeqLiftOverPsl.tName identifier altSeqExtSeqFiles "alternate sequence sequence files" hg38.altSeqLiftOverPsl.qName dupeOk hg38.seqNcbiAltSequence.acc hg38.extNcbiAltSequence.name chopAfter=. identifier ucscToRefSeq external=INSDC/RefSeq dependency "RefSeq accession names to UCSC chrom name translation" $gbd.chromInfo.chrom $gbd.ucscToRefSeq.chrom identifier ucscToINSDC external=INSDC dependency "INSDC names to UCSC chrom name translation" $gbd.chromInfo.chrom $gbd.ucscToINSDC.chrom identifier crispr10K "crispr 10K Ranges and Targets" $gbd.chromInfo.chrom $gbd.crispr10KRanges.chrom # to avoid the error on assemblies with Ensembl Gene scaffolds: # Error: 7771 duplicates in vicPac1.ensGene.name including 'ENSVPAT00000000004' # list on this avoid list: set notEnsemblTranscriptId2 !ce6,!ce9,!ce10,!ce11,!choHof1,!dipOrd1,!echTel1,!echTel2,!eriEur1,!eriEur2,!felCat3,!felCat8,!gadMor1,!macEug1,!macFas5,!manLeu1,!micMur1,!ochPri2,!ochPri3,!proCap1,!pteVam1,!sorAra1,!sorAra2,!tarSyr1,!tarSyr2,!tupBel1,!tupChi1,!vicPac1,!tupChi1,!vicPac2 #pulled this line into its own rule to reflect lack of dependency identifier ensemblTranscriptId2 external=Ensembl "Ensembl Transcript ID" $gbd,$notEnsemblTranscriptId2.ensGene.name chopAfter=. $ccdsDb.ccdsInfo.mrnaAcc minCheck=0.30 identifier ensemblTranscriptIdCe external=Ensembl dependency "Ensembl Transcript ID for C. elegans" $ce.ensGene.name dupeOk $ce.ensGtp.transcript minCheck=0.98 $ce.ensPep.name minCheck=0.98 $ce.ensemblToGeneName.name $ce.ensemblSource.name identifier ensemblTranscriptIdFelCat external=Ensembl dependency "Ensembl Transcript ID for felCat" $felCat.ensGene.name dupeOk $felCat.ensGtp.transcript minCheck=0.99 $felCat.ensPep.name minCheck=0.99 felCat3.ensemblToGeneName.name minCheck=0.99 felCat3.ensemblSource.name minCheck=0.99 # UCSC to Ensembl chrom name translation identifier ensemblLinkId external=Ensembl dependency "Ensembl Links from hgTracks" hg18,hg19,anoCar2,bosTau6,calJac3,oryCun2,panTro4,xenTro3,mm10,musFur1.chromInfo.chrom hg18,hg19,anoCar2,bosTau6,calJac3,oryCun2,panTro4,xenTro3,mm10,musFur1.ucscToEnsembl.ucsc identifier ucscToEnsembl external=Ensembl dependency "UCSC to Ensembl chrom name translation" hg18,hg19,panTro4.ucscToEnsembl.ensembl hg18,hg19,panTro4.ensemblLift.chrom # Ensembl EST identifier ensemblEstTranscriptId external=Ensembl dependency "Ensembl EST Transcript ID" $gbd.ensEstGene.name chopAfter=. $gbd.ensEstGtp.transcript chopAfter=. $gbd.ensEstPep.name chopAfter=. identifier gazeGeneId external=Genoscope "GAZE Gene ID" $gbd.gaze.name $gbd.gazePep.name # H-Invitational Database Identifiers identifier hinvTranscriptId external=H-INV dependency "H-Invitational Transcript ID" $hg.HInv.geneId $hg.knownToHInv.value $hg.HInvGeneMrna.qName # Protein Family Identifiers identifier pfamId external=Pfam fuzzy "Pfam (Protein Family) ID" $kgDb.knownToPfam.value dm1.bdgpToPfam.value identifier superfamilyId external=SCOP "Protein SCOP/Superfamily ID" hgFixed.scopDes.sunid $gbd.sfDes.id # This table is redundant with hgFixed.scopDes $gbd.sfAssign.sfID # Pathway Identifiers identifier bioCycMapId external=BioCyc "BioCyc Pathway Map ID" $gbd.bioCycMapDesc.mapID $gbd.bioCycPathway.mapID minCheck=0.78 identifier keggMapId external=KEGG "KEGG Pathway Map ID" $gbd.keggMapDesc.mapID dupeOk $gbd.keggPathway.mapID $gbd.knownToKeggEntrez.value $gbd.rgdGene2ToKeggEntrez.value identifier cgapId "NCI Cancer Genome Annotation Project Gene ID" $gbd.cgapAlias.cgapID dupeOk $gbd.cgapBiocPathway.cgapID identifier cgapMapId "NCI Cancer Genome Annotation Project Map ID" $gbd.cgapBiocDesc.mapID $gbd.cgapBiocPathway.mapID identifier cgapAlias "NCI Cancer Genome Annotation Project Alias" $gbd.cgapAlias.alias dupeOk $gbd,!hg16,!hg18,!hg19,!mm9,!mm10,!hg38.knownGene.name minCheck=0.50 hg16.knownGene.name minCheck=0.05 hg18,hg19,hg38,mm9,mm10.kgXref.geneSymbol minCheck=0.65 # SNP (Simple Nucleotide Polymorphism) Stuff identifier affySnp10KId external=Affymetrix "Affymetrix 10K SNP Identifier" hgFixed.affy10KDetails.affyId $hg.affy10K.name identifier affySnp120KId external=Affymetrix "Affymetrix 120K SNP Identifier" hgFixed.affy120KDetails.affyId $hg.affy120K.name identifier dbSnpId external=dbSNP fuzzy "NCBI dbSNP ID" $kgDb.knownToCdsSnp.value identifier dbSnpHgId typeOf=dbSnpId "Human dbSNP ID" hgFixed.dbSnpRsHg.rsId $hg.snpMap.name minCheck=0.90 hgFixed.affy10KDetails.rsId minCheck=0.94 hgFixed.affy120KDetails.rsId minCheck=0.97 identifier dbSnpMmId typeOf=dbSnpId "Mouse dbSNP ID" hgFixed.dbSnpRsMm.rsId $mm.snpMap.name identifier dbSnpRnId typeOf=dbSnpId "Rat dbSNP ID" hgFixed.dbSnpRsRn.rsId $rn.snpMap.name identifier hapmapSnpIdPhaseII "HapMap Phase II SNPs" hg17.hapmapAllelesSummary.name hg17.hapmapSnpsCEU.name hg17.hapmapSnpsCHB.name hg17.hapmapSnpsJPT.name hg17.hapmapSnpsYRI.name hg17.hapmapAllelesChimp.name hg17.hapmapAllelesMacaque.name identifier hapmapSnpIdPhaseIII "HapMap Phase III SNPs" # duplicates due to pseudo-autosomal regions: hg18,hg19.hapmapPhaseIIISummary.name dupeOk hg18,hg19.hapmapSnpsCEU.name hg18,hg19.hapmapSnpsCHB.name hg18,hg19.hapmapSnpsJPT.name hg18,hg19.hapmapSnpsYRI.name hg18,hg19.hapmapAllelesChimp.name hg18,hg19.hapmapAllelesMacaque.name hg18,hg19.hapmapLdCeu.name unique minCheck=0.999 hg18,hg19.hapmapLdChb.name unique minCheck=0.999 hg18,hg19.hapmapLdChbJpt.name unique minCheck=0.999 hg18,hg19.hapmapLdJpt.name unique minCheck=0.999 hg18,hg19.hapmapLdYri.name unique minCheck=0.999 hg18,hg19.hapmapLdPhCeu.name unique minCheck=0.999 hg18,hg19.hapmapLdPhChbJpt.name unique minCheck=0.999 hg18,hg19.hapmapLdPhYri.name unique minCheck=0.999 identifier snpAnnotations125 "SNP annotations" $snpDb125.snp125.name dupeOk $snpDb125.snp125Exceptions.name $snpDb125.snpSeq.acc minCheck=.8 hg17.snpArrayAffy10.rsId minCheck=0.98 hg17.snpArrayAffy10v2.rsId minCheck=0.98 hg17.snpArrayAffy250Nsp.rsId minCheck=0.98 hg17.snpArrayAffy250Sty.rsId minCheck=0.98 hg17.snpArrayAffy50HindIII.rsId minCheck=0.98 hg17.snpArrayAffy50XbaI.rsId minCheck=0.98 hg17.snpArrayIllumina300.name identifier snpAnnotations126 "SNP annotations" $snpDb126.snp126.name dupeOk $snpDb126.snp126Exceptions.name $snpDb126.snpSeq.acc minCheck=.8 hg18.snp126ortho.name hg18.snp126orthoPanTro2RheMac2.name hg18.snpArrayAffy5.rsId minCheck=0.98 hg18.snpArrayAffy6.rsId minCheck=0.98 hg18.snpArrayAffy250Nsp.rsId hg18.snpArrayAffy250Sty.rsId hg18.snpArrayIllumina300.name hg18.snpArrayIllumina550.name hg18.snpArrayIllumina650.name identifier snpAnnotations127 "SNP annotations" $snpDb127.snp127.name dupeOk $snpDb127.snp127Exceptions.name $snpDb127.snpSeq.acc minCheck=.8 identifier snpName128 "dbSNP version 128 rs* identifiers" $gbd.snp128.name dupeOk $gbd.snp128Exceptions.name $gbd.snp128Seq.acc minCheck=.9 hg18.snp128OrthoPanTro2RheMac2.name identifier snpExceptions128 "Annotations of unusual conditions in dbSNP version 128" $gbd.snp128ExceptionDesc.exception $gbd.snp128Exceptions.exception identifier snpName129 "dbSNP version 129 rs* identifiers" $gbd.snp129.name dupeOk $gbd.snp129Exceptions.name minCheck=.99 $gbd.snp129Seq.acc minCheck=.99 hg18.snp129OrthoPt2Pa2Rm2.name hg18.snpArrayIllumina1M.name minCheck=0.95 identifier snpExceptions129 "Annotations of unusual conditions in dbSNP version 129" $gbd.snp129ExceptionDesc.exception $gbd.snp129Exceptions.exception identifier snpName130 "dbSNP version 130 rs* identifiers" $gbd.snp130.name dupeOk $gbd.snp130Exceptions.name minCheck=.999 $gbd.snp130Seq.acc minCheck=.98 $gbd.snp130CodingDbSnp.name minCheck=.99 $hg.snp130OrthoPt2Pa2Rm2.name hg18.snpArrayIlluminaHuman660W_Quad.name minCheck=0.90 hg18.snpArrayIlluminaHumanCytoSNP_12.name minCheck=0.95 hg18.snpArrayIlluminaHumanOmni1_Quad.name minCheck=0.85 # gwasCatalog SNPs were mapped to hg18 using snp130: hg18.gwasCatalog.name identifier snpExceptions130 "Annotations of unusual conditions in dbSNP version 130" $gbd.snp130ExceptionDesc.exception $gbd.snp130Exceptions.exception identifier snpName131 "dbSNP version 131 rs* identifiers" $gbd.snp131.name dupeOk $gbd.snp131Exceptions.name minCheck=.999 $gbd.snp131Seq.acc minCheck=.93 $gbd.snp131CodingDbSnp.name minCheck=.90 $hg.snp131OrthoPt2Pa2Rm2.name hg18.snpArrayIlluminaHuman660W_Quad.name minCheck=0.90 hg18.snpArrayIlluminaHumanCytoSNP_12.name minCheck=0.95 hg18.snpArrayIlluminaHumanOmni1_Quad.name minCheck=0.85 identifier snpExceptions131 "Annotations of unusual conditions in dbSNP version 131" $gbd.snp131ExceptionDesc.exception $gbd.snp131Exceptions.exception identifier snpName132 "dbSNP version 132 rs* identifiers" $gbd.snp132.name dupeOk $gbd.snp132Common.name $gbd.snp132Flagged.name $gbd.snp132Mult.name $gbd.snp132Seq.acc minCheck=.98 $gbd.snp132CodingDbSnp.name minCheck=.90 $hg.snp132OrthoPt2Pa2Rm2.name identifier snpException132 "Exceptions that UCSC annotated on dbSNP version 132" $gbd.snp132ExceptionDesc.exception $gbd.snp132.exceptions comma $gbd.snp132Common.exceptions comma $gbd.snp132Flagged.exceptions comma $gbd.snp132Mult.exceptions comma identifier snpName135 "dbSNP version 135 rs* identifiers" $gbd.snp135.name dupeOk $gbd.snp135Common.name $gbd.snp135Flagged.name $gbd.snp135Mult.name $gbd.snp135Seq.acc minCheck=.98 $gbd.snp135CodingDbSnp.name minCheck=.90 $hg.snp135OrthoPt3Pa2Rm2.name identifier snpException135 "Exceptions that UCSC annotated on dbSNP version 135" $gbd.snp135ExceptionDesc.exception $gbd.snp135.exceptions comma $gbd.snp135Common.exceptions comma $gbd.snp135Flagged.exceptions comma $gbd.snp135Mult.exceptions comma identifier snpName137 "dbSNP version 137 rs* identifiers" $gbd.snp137.name dupeOk $gbd.snp137Common.name $gbd.snp137Flagged.name $gbd.snp137Mult.name $gbd.snp137Seq.acc minCheck=.98 $gbd.snp137CodingDbSnp.name minCheck=.90 $hg.snp137OrthoPt3Pa2Rm2.name identifier snpException137 "Exceptions that UCSC annotated on dbSNP version 137" $gbd.snp137ExceptionDesc.exception $gbd.snp137.exceptions comma $gbd.snp137Common.exceptions comma $gbd.snp137Flagged.exceptions comma $gbd.snp137Mult.exceptions comma identifier snpName138 "dbSNP version 138 rs* identifiers" $gbd.snp138.name dupeOk $gbd.snp138Common.name $gbd.snp138Flagged.name $gbd.snp138Mult.name $gbd.snp138Seq.acc minCheck=.98 $gbd.snp138CodingDbSnp.name minCheck=.90 $hg.snp138OrthoPt4Pa2Rm3.name identifier snpException138 "Exceptions that UCSC annotated on dbSNP version 138" $gbd.snp138ExceptionDesc.exception $gbd.snp138.exceptions comma $gbd.snp138Common.exceptions comma $gbd.snp138Flagged.exceptions comma $gbd.snp138Mult.exceptions comma identifier snpName141 "dbSNP version 141 rs* identifiers" $gbd.snp141.name dupeOk $gbd.snp141Common.name $gbd.snp141Flagged.name $gbd.snp141Mult.name $gbd.snp141Seq.acc minCheck=.98 $gbd.snp141CodingDbSnp.name minCheck=.90 $hg.snp141OrthoPt4Pa2Rm3.name identifier snpException141 "Exceptions that UCSC annotated on dbSNP version 141" $gbd.snp141ExceptionDesc.exception $gbd.snp141.exceptions comma $gbd.snp141Common.exceptions comma $gbd.snp141Flagged.exceptions comma $gbd.snp141Mult.exceptions comma identifier snpName142 "dbSNP version 142 rs* identifiers" $gbd.snp142.name dupeOk $gbd.snp142Common.name $gbd.snp142Flagged.name $gbd.snp142Mult.name $gbd.snp142Seq.acc minCheck=.98 $gbd.snp142CodingDbSnp.name minCheck=.90 $hg.snp142OrthoPt4Pa2Rm3.name identifier snpException142 "Exceptions that UCSC annotated on dbSNP version 142" $gbd.snp142ExceptionDesc.exception $gbd.snp142.exceptions comma $gbd.snp142Common.exceptions comma $gbd.snp142Flagged.exceptions comma $gbd.snp142Mult.exceptions comma identifier snpName144 "dbSNP version 144 rs* identifiers" $gbd.snp144.name dupeOk $gbd.snp144Common.name $gbd.snp144Flagged.name $gbd.snp144Mult.name $gbd.snp144Seq.acc minCheck=.98 $gbd.snp144CodingDbSnp.name minCheck=.90 $hg.snp144OrthoPt4Pa2Rm3.name # gwasCatalog SNPs were mapped to hg19/hg38 using snp144. Move this down to snp146 # and update trackDb settings if we remap to new dbSNP version: hg19.gwasCatalog.name minCheck=0.99 hg38.gwasCatalog.name minCheck=0.99 identifier snpException144 "Exceptions that UCSC annotated on dbSNP version 144" $gbd.snp144ExceptionDesc.exception $gbd.snp144.exceptions comma $gbd.snp144Common.exceptions comma $gbd.snp144Flagged.exceptions comma $gbd.snp144Mult.exceptions comma identifier snpName146 "dbSNP version 146 rs* identifiers" $gbd.snp146.name dupeOk $gbd.snp146Common.name $gbd.snp146Flagged.name $gbd.snp146Mult.name $gbd.snp146Seq.acc minCheck=.98 $gbd.snp146CodingDbSnp.name minCheck=.90 $hg.snp146OrthoPt4Pa2Rm3.name identifier snpException146 "Exceptions that UCSC annotated on dbSNP version 146" $gbd.snp146ExceptionDesc.exception $gbd.snp146.exceptions comma $gbd.snp146Common.exceptions comma $gbd.snp146Flagged.exceptions comma $gbd.snp146Mult.exceptions comma identifier snpName147 "dbSNP version 147 rs* identifiers" $gbd.snp147.name dupeOk $gbd.snp147Common.name $gbd.snp147Flagged.name $gbd.snp147Mult.name $gbd.snp147Seq.acc minCheck=.98 $gbd.snp147CodingDbSnp.name minCheck=.90 $hg.snp147OrthoPt4Pa2Rm3.name identifier snpException147 "Exceptions that UCSC annotated on dbSNP version 147" $gbd.snp147ExceptionDesc.exception $gbd.snp147.exceptions comma $gbd.snp147Common.exceptions comma $gbd.snp147Flagged.exceptions comma $gbd.snp147Mult.exceptions comma identifier snpName148 "dbSNP version 148 rs* identifiers" $gbd.snp148.name dupeOk $gbd.snp148Common.name $gbd.snp148Flagged.name $gbd.snp148Mult.name $gbd.snp148Seq.acc minCheck=.98 $gbd.snp148CodingDbSnp.name minCheck=.90 $hg.snp148OrthoPt4Pa2Rm3.name identifier snpException148 "Exceptions that UCSC annotated on dbSNP version 148" $gbd.snp148ExceptionDesc.exception $gbd.snp148.exceptions comma $gbd.snp148Common.exceptions comma $gbd.snp148Flagged.exceptions comma $gbd.snp148Mult.exceptions comma identifier snpName149 "dbSNP version 149 rs* identifiers" $gbd.snp149.name dupeOk $gbd.snp149Common.name $gbd.snp149Flagged.name $gbd.snp149Mult.name $gbd.snp149Seq.acc minCheck=.98 $gbd.snp149CodingDbSnp.name minCheck=.90 $hg.snp149OrthoPt4Pa2Rm3.name identifier snpException149 "Exceptions that UCSC annotated on dbSNP version 149" $gbd.snp149ExceptionDesc.exception $gbd.snp149.exceptions comma $gbd.snp149Common.exceptions comma $gbd.snp149Flagged.exceptions comma $gbd.snp149Mult.exceptions comma identifier snpName150 "dbSNP version 150 rs* identifiers" $hg.snp150.name dupeOk $hg.snp150Common.name $hg.snp150Flagged.name $hg.snp150Mult.name $hg.snp150Seq.acc minCheck=.98 $hg.snp150CodingDbSnp.name minCheck=.90 $hg.snp150OrthoPt5Pa2Rm8.name identifier snpException150 "Exceptions that UCSC annotated on dbSNP version 150" $hg.snp150ExceptionDesc.exception $hg.snp150.exceptions comma $hg.snp150Common.exceptions comma $hg.snp150Flagged.exceptions comma $hg.snp150Mult.exceptions comma identifier snpName151 "dbSNP version 151 rs* identifiers" $hg.snp151.name dupeOk $hg.snp151Common.name $hg.snp151Flagged.name $hg.snp151Mult.name hg38.snp151Seq.acc minCheck=.99 hg19.snp151Seq.acc minCheck=.96 $hg.snp151CodingDbSnp.name minCheck=.90 $hg.snp151OrthoPt5Pa2Rm8.name identifier snpException151 "Exceptions that UCSC annotated on dbSNP version 151" $hg.snp151ExceptionDesc.exception $hg.snp151.exceptions comma $hg.snp151Common.exceptions comma $hg.snp151Flagged.exceptions comma $hg.snp151Mult.exceptions comma identifier snpediaId "snpedia rs* identifiers" $hg.snpedia.name dupeOk $hg.snpediaHtml.name # Other NCBI Identifiers identifier locusLinkId external=LocusLink "NCBI LocusLink ID" hgFixed.refLink.locusLinkId dupeOk $gbd.keggPathway.locusID minCheck=0.98 $kgDb,!hg16,!mm8.knownToLocusLink.value minCheck=0.98 hg16,mm8.knownToLocusLink.value minCheck=0.96 $hg.omim2gene.geneId minCheck=0.60 $rn.rgdGene2ToLocusLink.value minCheck=0.70 identifier omimLocationId external=OMIM "Online Mendelian Inheritance in Man (OMIM) Location ID" $hg.omimLocation.name dupeOk exclude=0 $hg.omimGeneMap.omimId full minCheck=0.07 $hg.omimGeneMap2.omimId full minCheck=0.07 identifier omimAvSnpId external=OMIM "Online Mendelian Inheritance in Man (OMIM) AV SNP ID" $hg.omimAvSnp.name dupeOk exclude=0 identifier omimId external=OMIM "Online Mendelian Inheritance in Man (OMIM) ID" hgFixed.refLink.omimId dupeOk exclude=0 $hg.omimGene2.name minCheck=0.90 $hg.omimPhenotype.omimId minCheck=0.75 $hg.omimGeneMap.omimId minCheck=0.85 $hg.omimGeneMap2.omimId minCheck=0.85 $hg.omim2gene.omimId minCheck=0.60 identifier omimAvId external=OMIM "Online Mendelian Inheritance in Man (OMIM) AV ID" $hg.omimAv.avId dupeOk exclude=0 $hg.omimAvRepl.avId minCheck=0.90 $hg.omimAvSnp.name minCheck=0.90 identifier omimGene2Id "omimGene2 ID" $hg.omimGene2.name dupeOk $hg.omimGeneSymbol.omimId minCheck=0.90 $hg.omimAv.omimId minCheck=0.90 $hg.omimAvRepl.omimId minCheck=0.90 $hg.omimPhenotype.omimId minCheck=0.75 hgFixed.refLink.omimId exclude=0 minCheck=0.98 $hg.omim2gene.omimId minCheck=0.60 identifier omimPhenotypeId "OMIM Phenotype ID" $hg.omimPhenotype.phenotypeId dupeOk identifier evoCpgId "Evo Cpg ID" $hg.evoCpg.name dupeOk identifier unigeneId fuzzy "NCBI UniGene Cluster ID" # hgFixed.sage.uni $hg.uniGene_2.name chopBefore=. $hg.sage.uni identifier unigeneId2 external=UniGene "NCBI UniGene Cluster ID for databases with UniGene seq table entry" $gbd.seq.acc $galGal.uniGene_gg.qName $danRer.uniGene_dr.qName $hg.uniGene_3.qName identifier kiddEichlerId external=EichlerLab "Clone accession used in Kidd..Eichler '08" $hg.kiddEichlerToNcbi.name $hg.kiddEichlerDiscAbc7.name chopAfter=, minCheck=0.80 $hg.kiddEichlerDiscAbc8.name chopAfter=, $hg.kiddEichlerDiscAbc9.name chopAfter=, $hg.kiddEichlerDiscAbc10.name chopAfter=, $hg.kiddEichlerDiscAbc11.name chopAfter=, $hg.kiddEichlerDiscAbc12.name chopAfter=, $hg.kiddEichlerDiscAbc13.name chopAfter=, $hg.kiddEichlerDiscAbc14.name chopAfter=, hg17.kiddEichlerDiscG248.name chopAfter=, chopBefore=_ minCheck=0.01 $hg,!hg17.kiddEichlerDiscG248.name chopAfter=, chopBefore=_ minCheck=0.005 # BGI SNP Identifiers identifier bgiSnpId external=BGI "BGI SNP ID" $galGal.bgiSnp.name $galGal.bgiGeneSnp.snpName identifier bgiGeneId external=BGI "BGI Gene ID" $galGal.bgiGene.name $galGal.bgiGeneInfo.name minCheck=0.1 $galGal.bgiGenePep.name minCheck=0.95 $galGal.bgiGeneSnp.geneName minCheck=0.1 # Other Identifiers identifier mm10Patch1ExtFileId "External file ID for mm10 patch1 sequences" mm10.extMm10Patch1.id mm10.seqMm10Patch1.extFile identifier hg19Patch13ExtFileId "External file ID for hg19 patch13 sequences" hg19.extHg19Patch13.id hg19.seqHg19Patch13.extFile identifier hg19Patch10ExtFileId "External file ID for hg19 patch10 sequences" hg19.extHg19Patch10.id hg19.seqHg19Patch10.extFile identifier hg19Patch9ExtFileId "External file ID for hg19 patch9 sequences" hg19.extHg19Patch9.id hg19.seqHg19Patch9.extFile identifier hg19Patch5ExtFileId "External file ID for hg19 patch5 sequences" hg19.extHg19Patch5.id hg19.seqHg19Patch5.extFile identifier hg19Patch2ExtFileId "External file ID for hg19 patch2 sequences" hg19.extHg19Patch2.id hg19.seqHg19Patch2.extFile identifier hg38Patch11ExtFileId "External file ID for hg38 patch11 sequences" hg38.extHg38Patch11.id hg38.seqHg38Patch11.extFile identifier hg38Patch9ExtFileId "External file ID for hg38 patch9 sequences" hg38.extHg38Patch9.id hg38.seqHg38Patch9.extFile identifier hg38Patch7ExtFileId "External file ID for hg38 patch7 sequences" hg38.extHg38Patch7.id hg38.seqHg38Patch7.extFile identifier hg38Patch6ExtFileId "External file ID for hg38 patch6 sequences" hg38.extHg38Patch6.id hg38.seqHg38Patch6.extFile identifier hg38Patch5ExtFileId "External file ID for hg38 patch5 sequences" hg38.extHg38Patch5.id hg38.seqHg38Patch5.extFile identifier hg38Patch3ExtFileId "External file ID for hg38 patch3 sequences" hg38.extHg38Patch3.id hg38.seqHg38Patch3.extFile identifier hg38Patch2ExtFileId "External file ID for hg38 patch2 sequences" hg38.extHg38Patch2.id hg38.seqHg38Patch2.extFile identifier extFileId "External file ID" $gbd.extFile.id $gbd.seq.extFile rn3.multizHg15Mm3.extFile $sacCer.multizYeast.extFile $dm.a_gambiae_mypa.extFile $dm.d_pseudoobscura_mypa.extFile $dm.d_yakuba_mypa.extFile #$gbd.multiz4way.extFile #$gbd.multiz5way.extFile #$gbd.multiz6way.extFile #$gbd.multiz7way.extFile #$gbd.multiz8way.extFile #$gbd.multiz9way.extFile #$gbd.multiz10way.extFile #$gbd.multiz11way.extFile #$gbd.multiz12way.extFile #$gbd.multiz15way.extFile #$gbd.multiz17way.extFile #$gbd.multiz28way.extFile identifier gbExtFileId "External file ID for GenBank incremental update system" hgFixed.gbExtFile.id hgFixed.gbSeq.gbExtFile minCheck=0.85 identifier encodeRegion "ENCODE (extensive analysis of 1% of genome) Region" hgFixed.encodeRegionInfo.name $hg.encodeRegions.name identifier blastDm1FBPepId "dm1 proteins" dm1.blastFBPep00.name $anoGam.blastDm1FB.qName $apiMel.blastDm1FB.qName $dp.blastDm1FB.qName $droYak.blastDm1FB.qName $droMult.blastDm1FB.qName identifier blastDm2FBPepId dependency "dm2 proteins" dm2.blastFBPep01.name $anoGam.blastDm2FB.qName $apiMel.blastDm2FB.qName $dp.blastDm2FB.qName $droYak.blastDm2FB.qName $droMult.blastDm2FB.qName identifier blastHg16KGPepId "hg16 proteins" hg16.blastKGPep00.name sacCer1.blastHg16KG.qName ce2.blastHg16KG.qName ci1.blastHg16KG.qName cioSav1.blastHg16KG.qName dm1.blastHg16KG.qName galGal2.blastHg16KG.qName identifier blastHg16KGRefId "hg16 ref 00" hg16.blastKGRef00.acc sacCer1.blastHg16KG.qName ce2.blastHg16KG.qName ci1.blastHg16KG.qName cioSav1.blastHg16KG.qName dm1.blastHg16KG.qName galGal2.blastHg16KG.qName # identifier blastHg17KGPep00Id (knownGene upgraded) # "hg17 proteins 00" # $hg.blastKGPep00.name # $xenTro.blastHg17KG.qName identifier blastKG01 "hg17 proteins 01" $gbd.blastHg17KG.qName dupeOk hg17.blastKGPep01.name hg17.blastKGRef01.acc identifier blastHg17KGPep01Id "hg17 peptides 01" hg17.blastKGPep01.name hg17.knownGene.name minCheck=0.30 hg17.blastKGRef01.acc full monDom1.blastHg17KG.qName fr1.blastHg17KG.qName tetNig1.blastHg17KG.qName xenTro1.blastHg17KG.qName identifier blastHg17KGRef01Id "hg17 ref 01" hg17.blastKGRef01.acc monDom1.blastHg17KG.qName fr1.blastHg17KG.qName tetNig1.blastHg17KG.qName xenTro1.blastHg17KG.qName identifier blastHg17KGPep02Id "hg17 peptides 02" hg17.blastKGPep02.name hg17.knownGene.name minCheck=0.95 hg17.blastKGRef02.acc full danRer3.blastHg17KG.qName bosTau2.blastHg17KG.qName canFam2.blastHg17KG.qName apiMel2.blastHg17KG.qName dm2.blastHg17KG.qName identifier blastHg17KGRef02Id "hg17 ref 02" hg17.blastKGRef02.acc danRer3.blastHg17KG.qName bosTau2.blastHg17KG.qName canFam2.blastHg17KG.qName apiMel2.blastHg17KG.qName dm2.blastHg17KG.qName identifier blastHg18KGPep04Id "hg18 peptides 04" hg18.blastKGPep04.name hg18.blastKGRef04.acc full hg18.knownGeneOld2.name minCheck=0.95 monDom4.blastHg18KG.qName galGal3.blastHg18KG.qName xenTro2.blastHg18KG.qName danRer4.blastHg18KG.qName danRer5.blastHg18KG.qName canFam2.blastHg18KG.qName felCat3.blastHg18KG.qName felCat4.blastHg18KG.qName dm2.blastHg18KG.qName fr2.blastHg18KG.qName mm8.blastHg18KG.qName ce4.blastHg18KG.qName ce10.blastHg18KG.qName dm3.blastHg18KG.qName strPur1.blastHg18KG.qName strPur2.blastHg18KG.qName bosTau2.blastHg18KG.qName ornAna1.blastHg18KG.qName equCab1.blastHg18KG.qName equCab2.blastHg18KG.qName anoCar1.blastHg18KG.qName gasAcu1.blastHg18KG.qName bosTau3.blastHg18KG.qName bosTau4.blastHg18KG.qName tetNig1.blastHg18KG.qName tetNig2.blastHg18KG.qName taeGut1.blastHg18KG.qName oryLat2.blastHg18KG.qName sacCer2.blastHg18KG.qName mm9.blastHg18KG.qName aplCal1.blastHg18KG.qName ailMel1.blastHg18KG.qName oryCun2.blastHg18KG.qName identifier blastHg18KGRef04Id "hg18 ref 04" hg18.blastKGRef04.acc hg18.knownGeneOld2.name minCheck=0.95 monDom4.blastHg18KG.qName galGal3.blastHg18KG.qName xenTro2.blastHg18KG.qName danRer4.blastHg18KG.qName danRer5.blastHg18KG.qName canFam2.blastHg18KG.qName felCat3.blastHg18KG.qName felCat4.blastHg18KG.qName dm2.blastHg18KG.qName fr2.blastHg18KG.qName mm8.blastHg18KG.qName ce4.blastHg18KG.qName ce10.blastHg18KG.qName dm3.blastHg18KG.qName strPur1.blastHg18KG.qName strPur2.blastHg18KG.qName bosTau2.blastHg18KG.qName ornAna1.blastHg18KG.qName equCab1.blastHg18KG.qName equCab2.blastHg18KG.qName anoCar1.blastHg18KG.qName gasAcu1.blastHg18KG.qName bosTau3.blastHg18KG.qName bosTau4.blastHg18KG.qName tetNig1.blastHg18KG.qName tetNig2.blastHg18KG.qName taeGut1.blastHg18KG.qName oryLat2.blastHg18KG.qName mm9.blastHg18KG.qName aplCal1.blastHg18KG.qName ailMel1.blastHg18KG.qName oryCun2.blastHg18KG.qName identifier blastHg17KGRef01SwissId "hg17 proteins swiss 01" $hg.blastKGRef01.extra1 dupeOk uniProt.displayId.acc identifier blastCe4SG01 "ce4 proteins 01" $gbd.blastCe6SG.qName dupeOk ce4.blastSGPep01.name ce4.blastSGRef01.acc identifier blastCe6SG01 "ce6 proteins 01" $gbd.blastCe6SG.qName dupeOk ce6.blastSGPep01.name ce6.blastSGRef01.acc identifier blastCe9SG01 "ce9 proteins 01" $gbd.blastCe9SG.qName dupeOk ce9.blastSGPep01.name ce9.blastSGRef01.acc identifier tfbsCons "transcription factor binding sites" $hg.tfbsConsSites.name dupeOk $hg.tfbsConsFactors.name identifier cosmic "Catalogue Of Somatic Mutations In Cancer" $hg.cosmic.name $hg.cosmicRaw.cosmic_mutation_id identifier esRegModule "Eran Segal's collection of motifs that appear together in a regulatory module" $sacCer.esRegModuleToMotif.module dupeOk $sacCer.esRegGeneToModule.module full minCheck=0.99 identifier esRegMotif "Eran Segal's motifs deduced from coregulated genes" $sacCer.esRegMotif.name $sacCer.esRegModuleToMotif.motif $sacCer.esRegGeneToMotif.name identifier yeastGrowthCondition "A growth condition for yeast cells" $sacCer.growthCondition.name $sacCer.transRegCodeCondition.growthCondition identifier transRegCode "Harbison, Gordon et al regulatory motifs and CHIP/CHIP data" $sacCer.transRegCodeCondition.name dupeOk $sacCer.transRegCodeMotif.name $sacCer.transRegCode.name $sacCer.transRegCodeProbe.tfList comma chopAfter=_ identifier anoEstTclId "AnoEST TCL* ID -- joins track and aux. table of expressed IDs" $anoGam.anoEstTcl.name $anoGam.anoEstExpressed.name minCheck=0.30 identifier allenBrainGene "KG link to Allen Brain Institute: Gene Expression in the Human Cortex" $gbd.kgXref.geneSymbol dupeOk $gbd.allenBrainGene.geneSymbol minCheck=0.95 identifier allenBrainProbe "A probe used in the Allen Brain Atlas" $gbd.allenBrainUrl.name $gbd.allenBrainAli.qName identifier jaxRepTranscriptName external=MGI "Jackson Labs/MGI Allele name: representative transcript ID" $mm.jaxRepTranscript.name dupeOk $mm.jaxRepTranscriptAlias.name identifier jaxAlleleName external=MGI "Jackson Labs/MGI Allele name: concatenated representative transcript ID and allele ID" # Using dupeOk here because there are some case-sensitive allele name diffs (ugh) $mm.jaxAllele.name dupeOk $mm.jaxAlleleInfo.name $mm.jaxAllelePheno.allele identifier jaxPhenotypeName external=MGI "Jackson Labs/MGI Phenotype name: representative transcript ID" $mm.jaxPhenotype.name dupeOk $mm.jaxPhenotypeAlias.name mm8,mm9,mm10.jaxAllelePheno.transcript minCheck=0.9 identifier jaxGeneTrapName external=MGI "Jackson Labs/MGI GeneTrap name: concatenated representative transcript ID and allele ID" $mm.jaxGeneTrap.name dupeOk $mm.jaxGeneTrapInfo.name #links between the UniProt variants tables identifier protVarId "UniProt Variants track mutation identifier for attributes and links" hg18.protVar.id hg18.protVarAttr.id hg18.protVarLink.id hg18.protVarPos.name #links between UniProt and the variants tables identifier protVarIdUni "UniProt Variants track mutation identifier contains UniProt ID" uniProt.protein.acc hg18.protVar.name chopAfter=: #links between gv (the new Locus Variants) and related tables identifier gvId "Locus Variants track mutation identifier for attributes and links" hgFixed.gv.id hgFixed.gvLink.id minCheck=0.95 hgFixed.gvAttr.id minCheck=0.98 hgFixed.gvAttrLong.id hg17,hg18.gvPos.name identifier gvSrcId "Locus Variants track source ID" hgFixed.gvSrc.srcId hgFixed.gv.srcId #links between oreganno (regulatory annotation) and related tables identifier oregId "ORegAnno track identifier: links annotations to attributes and external links" $hg,$dm,$sacCer,$mm,$canFam.oreganno.id $hg,$dm,$sacCer,$mm,$canFam.oregannoAttr.id $hg,$dm,$sacCer,$mm,$canFam.oregannoLink.id # retroposon track, dbRIP_* and polyGenotype table link identifier dbRIPNameAlu fuzzy "Retroposon, dbRIP database name id to polymorphism statistics link" hg17.dbRIPAlu.name unique hg17.polyGenotype.name identifier dbRIPNameL1 fuzzy "Retroposon, dbRIP database name id to polymorphism statistics link" hg17.dbRIPL1.name unique hg17.polyGenotype.name identifier dbRIPNameSVA fuzzy "Retroposon, dbRIP database name id to polymorphism statistics link" hg17.dbRIPSVA.name unique hg17.polyGenotype.name identifier jkgTranscriptId "Known genes 3 trancript identifier" $hg,$mm.jkgTxCdsRepick.name $hg,$mm.jkgTxInfo.name $hg,$mm.jkgTxCdsEvidence.name #links between omicia and links and attributes tables identifier omiciaHg18Id "Omicia track identifier: links annotations to attributes and external links" hg18.omicia.name hg18.omiciaAttr.id hg18.omiciaLink.id identifier hg18ContigDiff "contig difference track" hg18.gold.frag dupeOk $split hg18.hg18ContigDiff.name identifier hg19ContigDiff "contig difference track" hg19.gold.frag dupeOk hg19.hg19ContigDiff.name identifier ContigDiff "contig difference track" hg19,hg38.gold.frag dupeOk hg19,hg38.hg38ContigDiff.name # lsSnpPdb tables identifier lsSnpPdbProtId "lsSnpPdb table protId field" uniProt.extDbRef.acc dupeOk $lsSnpDb.lsSnpPdb.protId identifier lsSnpPdbKgId "lsSnpPdb table protId field" $lsSnpDb.kgXref.spID dupeOk $lsSnpDb.lsSnpPdb.protId minCheck=0.99 identifier lsSnpPdbPdbId "lsSnpPdb table pdbId field" uniProt.extDbRef.extAcc1 dupeOk $lsSnpDb.lsSnpPdb.pdbId minCheck=0.99 identifier lsSnpPdbSnpHg18 "lsSnpPdb table snpId field" hg18.snp130.name dupeOk hg18.lsSnpPdb.snpId identifier lsSnpPdbSnpHg19 "lsSnpPdb table snpId field" hg19.snp131.name dupeOk hg19.lsSnpPdb.snpId identifier consIndelsId "consIndels tables name field" hg17,hg18,hg19.consIndelsHgMmCanFam.name hg17,hg18,hg19.consIndelsHgMmCanFamConf.id # publication track info identifier pubsArticleId external=pubTools "internal ID of article, this is different from pubmed, doi or piis, generated during download " $gbd.pubsBlat.name dupeOk $gbd.pubsBlatPsl.articleId hgFixed.pubsSequenceAnnot.articleId hgFixed.pubsMarkerAnnot.articleId hgFixed.pubsArticle.articleId identifier pubsSequenceId external=pubTools "ID of sequence found in article " hgFixed.pubsSequence.annotId dupeOk $gbd.pubsBlat.seqIds comma $gbd.pubsBlatPsl.qName identifier pubsMarkerId "keyword ('marker') found in an article, like a SNP/band/gene/etc" hgFixed.pubsMarkerAnnot.markerId dupeOk $gbd.pubsMarkerBand.name $gbd.pubsMarkerSnp.name $gbd.pubsMarkerGene.name # web sequences track identifier pubsBingArticleId external=pubTools " internal ID of webpage, identifies a URL " $gbd.pubsBingBlat.name dupeOk $gbd.pubsBingBlatPsl.articleId hgFixed.pubsBingArticle.articleId hgFixed.pubsBingSequenceAnnot.articleId identifier pubsBingSequenceId external=pubTools "ID of sequence found in webpage " hgFixed.pubsBingSequence.annotId dupeOk $gbd.pubsBingBlat.seqIds comma $gbd.pubsBingBlatPsl.qName identifier ceuBcellRNASeqId "ID of ceuBcellRNASeq" $hg.ceuBcellRNASeq.name dupeOk identifier geneReviewsId "GeneReviews article ID" hg18,hg19,hg38.kgXref.geneSymbol dupeOk hg18,hg19,hg38.geneReviews.name minCheck=0.85 identifier geneReviewsRefGeneId "ID of GeneReviewsRefGene" hg18,hg19,hg38.kgXref.geneSymbol dupeOk hg18,hg19,hg38.geneReviewsDetail.geneSymbol minCheck=0.85 identifier mm10Strains1ExtFileId "External file ID for mm10 strain1 sequences" mm10.extMm10Strains1.id mm10.seqMm10Strains1.extFile identifier mouseStrains "chrom names in the mouse alternate strains" mm10.chromInfo.chrom mm10.altSeqLiftOverPslStrains1.tName identifier lrgTranscriptId "ID of Locus Reference Genomic (LRG) transcript" $hg.lrgTranscriptAli.qName dupeOk $hg.lrgCdna.name $hg.lrgPep.name $hg.lrgCds.id identifier rmskJoinedCurrent "linking together RepeatMasker repeat fragments rmskJoined" $gbd.rmskAlignCurrent.id dupeOk $gbd.rmskJoinedCurrent.id minCheck=0.99 $gbd.rmskOutCurrent.id minCheck=0.99 identifier rmskJoinedBaseline "linking together RepeatMasker repeat fragments rmskJoined" $gbd.rmskAlignBaseline.id dupeOk $gbd.rmskJoinedBaseline.id $gbd.rmskOutBaseline.id identifier dnaseMasterSourceId "Numeric index of cell type contributing to a DNAse master site" hg19.wgEncodeAwgDnaseMasterSources.id hg19.wgEncodeAwgDnaseMasterSites.sourceIds comma full identifier dnaseClusterSourceId "Numeric index of cell type contributing to a DNAse cluster" $hg.wgEncodeRegDnaseClusteredSources.id hg19.wgEncodeRegDnaseClusteredV3.sourceIds comma full hg38.wgEncodeRegDnaseClustered.sourceIds comma full identifier peptideAtlasAccession external=PeptideAtlas "Peptide accession from peptideatlas.org" hgFixed.peptideAtlas2014Peptides.accession hg19.peptideAtlas2014.name # Transcription Factor and TF Motif track info identifier txnFactorGeneId "Transcription factor gene name (for human, HGNC)" hg19,hg38.encRegTfbsClustered.name dupeOk hg19.wgEncodeRegTfbsClusteredV3.name hg19.wgEncodeRegClusteredInputsV3.factor hg19,hg38.encRegTfbsClusteredInputs.factor hg19,hg38.factorbookMotifCanonical.target minCheck=.75 hg19,hg38.factorbookGeneAlias.name minCheck=0.75 identifier txnFactorClusterSourceId "Numeric id of a source contributing to a TFBS cluster" hg19,hg38.encRegTfbsClusteredSources.id hg19,hg38.encRegTfbsClustered.sourceIds comma identifier txnFactorClusterInputId "Identifier of a source contributing to a TFBS cluster" hg19,hg38.encRegTfbsClusteredSources.description hg19,hg38.encRegTfbsClusteredInputs.source identifier txnFactorMotifId "Transcription factor motif name/id" hg19.factorbookMotifPos.name dupeOk hg19.factorbookMotifPwm.name minCheck=0.85 hg19.factorbookMotifCanonical.motif comma minCheck=0.85 identifier ncbiGene "Genes on Ebola virus from genbank records" $eboVir,$staAur.ncbiGene.chrom dupeOk $eboVir.chromInfo.chrom $staAur.chromInfo.chrom identifier ncbiGeneDesc "Genes descriptions on Staph bacteria from genbank records" $staAur.ncbiGene.name dupeOk $staAur.geneDesc.name identifier ws245Genes "WS245 gene track" ce11.ws245Genes.name ce11.ws245GenesPeptide.name identifier ncbiRefSeq "NCBI RefSeq gene track" $gbd.ncbiRefSeq.name dupeOk $gbd.ncbiRefSeqLink.id full $gbd.ncbiRefSeqCurated.name $gbd.ncbiRefSeqHgmd.name $gbd.ncbiRefSeqPredicted.name $gbd.ncbiRefSeqPsl.qName $gbd.ncbiRefSeqCds.id $gbd.seqNcbiRefSeq.acc identifier ncbiRefSeqPepTable "NCBI RefSeq protein sequences" $gbd.ncbiRefSeqPepTable.name $gbd.ncbiRefSeqLink.protAcc full exclude= identifier ncbiRefSeqRna "NCBI RefSeq RNA sequences" $gbd.extNcbiRefSeq.id $gbd.seqNcbiRefSeq.extFile full # GTEx (Genotype-Tissue Expression) identifier gtexDonor "GTEx donor ID" hgFixed.gtexDonor.name hgFixed.gtexSample.donor identifier gtexSample "GTEx sample ID" hgFixed.gtexSample.sampleId hgFixed.gtexSampleData.sample identifier gtexGeneId "GTEx gene ID (ENS gene)" hgFixed.gtexSampleData.geneId dupeOk hg19,hg38.gtexGene.geneId hg19,hg38.gtexGeneModel.name identifier gtexTissue "Short name for GTEx tissue (UCSC)" hgFixed.gtexSampleData.tissue dupeOk hgFixed.gtexTissue.name identifier chromAlias "Chromosome name correspondence to Ensembl, RefSeq, GenBank assemblies" $gbd.chromAlias.chrom dupeOk $gbd.chromInfo.chrom minCheck=0.99 # hgGeneGraph protein interaction viewer data tables identifier ggDoc "identifier of a publication, currently the PMID, an integer " hgFixed.ggDoc.docId minCheck=0.99 hgFixed.ggDocEvent.docId minCheck=0.99 hgFixed.ggEventDb.docIds separator=| minCheck=0.99 identifier ggEvent "an event (originally an NLP term) here is a protein interaction with a direction, from a curated database or from text mining." hgFixed.ggLinkEvent.eventId dupeOk hgFixed.ggEventDb.eventId minCheck=0.99 hgFixed.ggDocEvent.eventId minCheck=0.99 hgFixed.ggEventText.eventId identifier ggGeneSymbol "An HGNC gene symbol, but a few old synonyms slipped into these tables" hgFixed.ggGeneName.gene hgFixed.ggLink.gene1 minCheck=0.99 hgFixed.ggLink.gene2 minCheck=0.99 hgFixed.ggGeneClass.gene minCheck=0.97 # Dependencies not already captured in identifiers dependency $hg.gladHumESDistance $hg.knownToGnfAtlas2 hgFixed.gladHumESRatio dependency $mm.mouseLandscapeDistance $mm.knownToXM hgFixed.mouseLandscape dependency $mm.affyGnfU74ADistance $mm.knownToU74 hgFixed.gnfMouseU74aMedianRatio dependency $mm.affyGnfU74BDistance $mm.knownToU74 hgFixed.gnfMouseU74bMedianRatio dependency $mm.affyGnfU74CDistance $mm.knownToU74 hgFixed.gnfMouseU74cMedianRatio dependency $hg.gnfU95Distance $hg.knownToU95 hgFixed.gnfHumanU95MedianRatio dependency $hg.gnfAtlas2Distance $hg.knownToGnfAtlas2 hgFixed.gnfHumanAtlas2MedianRatio dependency $ce.kimExpDistance hgFixed.kimWormLifeMedianRatio dependency dm1.arbExpDistance dm1.bdgpToCanonical hgFixed.arbFlyLifeMedianRatio dependency $dm,!dm1.arbExpDistance $dm,!dm1.flyBaseToCG hgFixed.arbFlyLifeMedianRatio dependency $sacCer.choExpDistance hgFixed.yeastChoCellCycle # FAN says: the following hg17 tables are an exception dependency $pbDb,!hg17.pbAnomLimit $pbDb.knownGenePep dependency $pbDb,!hg17.pbResAvgStd $pbDb.knownGenePep dependency $pbDb,!hg17.pepCCntDist $pbDb.knownGenePep dependency $pbDb,!hg17.pepExonCntDist $pbDb.knownGenePep dependency $pbDb,!hg17.pepHydroDist $pbDb.knownGenePep dependency $pbDb,!hg17.pepIPCntDist $pbDb.knownGenePep dependency $pbDb,!hg17.pepMolWtDist $pbDb.knownGenePep dependency $pbDb,!hg17.pepPiDist $pbDb.knownGenePep dependency $pbDb,!hg17.pepResDist $pbDb.knownGenePep dependency $pbDb.pepMwAaDist $pbDb.knownGenePep dependency $pbDb.pbAaDistA $pbDb.knownGenePep dependency $pbDb.pbAaDistC $pbDb.knownGenePep dependency $pbDb.pbAaDistD $pbDb.knownGenePep dependency $pbDb.pbAaDistE $pbDb.knownGenePep dependency $pbDb.pbAaDistF $pbDb.knownGenePep dependency $pbDb.pbAaDistG $pbDb.knownGenePep dependency $pbDb.pbAaDistH $pbDb.knownGenePep dependency $pbDb.pbAaDistI $pbDb.knownGenePep dependency $pbDb.pbAaDistK $pbDb.knownGenePep dependency $pbDb.pbAaDistL $pbDb.knownGenePep dependency $pbDb.pbAaDistM $pbDb.knownGenePep dependency $pbDb.pbAaDistN $pbDb.knownGenePep dependency $pbDb.pbAaDistP $pbDb.knownGenePep dependency $pbDb.pbAaDistQ $pbDb.knownGenePep dependency $pbDb.pbAaDistR $pbDb.knownGenePep dependency $pbDb.pbAaDistS $pbDb.knownGenePep dependency $pbDb.pbAaDistT $pbDb.knownGenePep dependency $pbDb.pbAaDistV $pbDb.knownGenePep dependency $pbDb.pbAaDistW $pbDb.knownGenePep dependency $pbDb.pbAaDistY $pbDb.knownGenePep # Ignored tables - no linkage here that we check at least. tablesIgnored go instance_data source_audit tablesIgnored visiGene vgPrbAli vgPrbAliAll tableDescriptions tablesIgnored hgFixed omimTitle cutters rebaseRefs tablesIgnored $gbd NIAGene assemblyFrags affyDrosDev% ancientRepeat animalQtl augustusGene axtInfo bam% blatFr1 chromInfo cloneEnds% contamination cpgIsland% crisprRanges crisprTargets crispr10KTargets locusName ctgPos ctgPos2 cytoBand cytoBandIdeo evofold evofoldV2 exoniphy FaceBase24SampleTypesAvg firstEF gapOverlap gbLoaded gbDelete_tmp gc5Base gc5BaseBw gcPercent genomicSuperDups genscanSubopt %gold grp hgFindSpec% history intronEst knownAlt metaDb% microsat miRNA nestedRepeats nestedRepeatsRM327 numtSAssembled numtS numtSMitochondrion numtSMitochondrionChrPlacement patBulk patNonBulk qPcrPrimers quality qualityBw rnaCluster rnaGene regPotential% sangerGenefinder sangamoDnaseHs sangamoDnaseHsNeg sangamoDnaseHsPos simpleRepeat spAnnot spStruct windowmaskerSdust sgpGene tableDescriptions tandemDups tigrGeneIndex trackDb% chr%_mrna chr%_blastz% chr%_blat% chr%_gap chr%_rmsk chr%_rmskRM327 gap rmsk axtNet% blat% blast% repeats multiz%way multiz%waySummary multiz%wayFrames strainName%way strainName%wayFrames phyloP%way% phastCons%way% phastConsElements%way% strainPhastCons%way% strainPhastConsElements%way% strainPhyloP%way% tantan jaxQTL jaxQtl jaxQtlAsIs jaxQtlPadded ucscGenePfam uwNucOccA375 uwNucOccDennis uwNucOccMec ws210Gene ws245Genes gbCdnaInfo author cds cell description development gbLoaded geneName keyword library mrnaClone organism productName sex source tissue imageClone gbSeq gbExtFile gbMiscDiff gbWarn refSeqStatus refLink refSeqSummary gbStatus ncbiRefSeqOther splitOverlap tablesIgnored $kgDb pbAaDist_ pbAnomLimit pbResAvgStd pbStamp pep%Dist tablesIgnored hg38 altSeqLiftOverPslP2 altSeqLiftOverPslP3 altSeqLiftOverPslP6 altSeqLiftOverPslP7 centromeres coriellDelDup hg38Patch11Haplotypes hg38Patch11Patches hg38Patch9Haplotypes hg38Patch9Patches hg38Patch7Haplotypes hg38Patch7Patches hg38Patch6Haplotypes hg38Patch6Patches hg38Patch5Haplotypes hg38Patch5Patches hg38Patch3Haplotypes hg38Patch3Patches hg38Patch2Haplotypes hg38Patch2Patches lincRNAsCTAdipose lincRNAsCTAdrenal lincRNAsCTBrain lincRNAsCTBrain_R lincRNAsCTBreast lincRNAsCTColon lincRNAsCTForeskin_R lincRNAsCTHeart lincRNAsCTKidney lincRNAsCTLiver lincRNAsCTLung lincRNAsCTLymphNode lincRNAsCTOvary lincRNAsCTPlacenta_R lincRNAsCTProstate lincRNAsCTSkeletalMuscle lincRNAsCTTestes lincRNAsCTTestes_R lincRNAsCTThyroid lincRNAsCTWhiteBloodCell lincRNAsCThLF_r1 lincRNAsCThLF_r2 lincRNAsTranscripts wgEncodeGencode2wayConsPseudo% wgEncodeGencodePolya% tablesIgnored hg19 affyCytoScan affyExonProbe% allHg19RS_BW altSeqHaplotypes altSeqHaplotypesP9 altSeqLiftOverPsl altSeqLiftOverPslP9 altSeqPatches altSeqPatchesP9 altSeqPatchesP10 bacEndPairsBad bamAllNumtSSorted coriellDelDup gnomadVariants lincRNAsCTAdipose lincRNAsCTAdrenal lincRNAsCTBrain lincRNAsCTBrain_R lincRNAsCTBreast lincRNAsCTColon lincRNAsCTForeskin_R lincRNAsCTHeart lincRNAsCTKidney lincRNAsCTLiver lincRNAsCTLung lincRNAsCTLymphNode lincRNAsCTOvary lincRNAsCTPlacenta_R lincRNAsCTProstate lincRNAsCTSkeletalMuscle lincRNAsCTTestes lincRNAsCTTestes_R lincRNAsCTThyroid lincRNAsCTWhiteBloodCell lincRNAsCThLF_r1 lincRNAsCThLF_r2 lincRNAsTranscripts xlincRNAs multizMHCSummary netSyn_mann_hap4 net_dbb_hap3 net_apd_hap1 net_ssto_hap7 net_qbl_hap6 net_mcf_hap5 net_mann_hap4 net_haplotypes net_cox_hap2 net_chr4_ctg9_hap1 net_chr17_ctg5_hap1 netVenter1 netSyn_ssto_hap7 netSyn_qbl_hap netSyn_qbl_hap6 netSyn_mcf_hap5 netSyn_apd_hap1 netSyn_cox_hap2 netSyn_dbb_hap3 chain_ssto_hap7 chain_ssto_hap7Link hapRegions multizMHC chain_mcf_hap5Link chain_qbl_hap6 chain_qbl_hap6Link chain_haplotypesLink chain_mann_hap4 chain_mann_hap4Link chain_mcf_hap5 chain_chr4_ctg9_hap1 chain_chr4_ctg9_hap1Link chain_cox_hap2 chain_cox_hap2Link chain_dbb_hap3 chain_dbb_hap3Link chainVenter1 chainVenter1Link chain_apd_hap1 chain_apd_hap1Link chain_chr17_ctg5_hap1 chain_chr17_ctg5_hap1Link chain_haplotypes hinv70Coding hinv70NonCoding hinv70PseudoGene uMassBrainHistone% dhcBamDenisova dhcHumDerDenAncAllFixed dhcHumDerDenAncAllFixedDbSnp dhcHumDerDenAncAllHighFreq dhcHumDerDenAncCcdsFrameshiftCodingFixed dhcHumDerDenAncCcdsFrameshiftCodingFixedDbSnp dhcHumDerDenAncCcdsFrameshiftCodingHighFreq dhcHumDerDenAncCcdsInFrameNonsynFixed dhcHumDerDenAncCcdsNonsynFixed dhcHumDerDenAncCcdsNonsynFixedDbSnp dhcHumDerDenAncCcdsNonsynHighFreq dhcHumDerDenAncCcdsSpliceFixed dhcHumDerDenAncCcdsSpliceFixedDbSnp dhcHumDerDenAncCcdsSpliceHighFreq dhcHumDerDenAncCcdsSynFixed dhcHumDerDenAncCcdsSynFixedDbSnp dhcHumDerDenAncCcdsSynHighFreq dhcHumDerDenAncCcdsUtr3Fixed dhcHumDerDenAncCcdsUtr3FixedDbSnp dhcHumDerDenAncCcdsUtr3HighFreq dhcHumDerDenAncCcdsUtr5Fixed dhcHumDerDenAncCcdsUtr5FixedDbSnp dhcHumDerDenAncCcdsUtr5HighFreq dhcHumDerDenAncFrameshiftCodingFixed dhcHumDerDenAncFrameshiftCodingFixedDbSnp dhcHumDerDenAncFrameshiftCodingHighFreq dhcHumDerDenAncInFrameNonsynFixed dhcHumDerDenAncNonsynFixed dhcHumDerDenAncNonsynFixedDbSnp dhcHumDerDenAncNonsynHighFreq dhcHumDerDenAncRegFixed dhcHumDerDenAncRegFixedDbSnp dhcHumDerDenAncRegHighFreq dhcHumDerDenAncRegMotifFixed dhcHumDerDenAncRegMotifFixedDbSnp dhcHumDerDenAncRegMotifHighFreq dhcHumDerDenAncRegMotifHighInfoFixed dhcHumDerDenAncRegMotifHighInfoFixedDbSnp dhcHumDerDenAncRegMotifHighInfoHighFreq dhcHumDerDenAncSpliceFixed dhcHumDerDenAncSpliceFixedDbSnp dhcHumDerDenAncSpliceHighFreq dhcHumDerDenAncSynFixed dhcHumDerDenAncSynFixedDbSnp dhcHumDerDenAncSynHighFreq dhcHumDerDenAncUtr3Fixed dhcHumDerDenAncUtr3FixedDbSnp dhcHumDerDenAncUtr3HighFreq dhcHumDerDenAncUtr5Fixed dhcHumDerDenAncUtr5FixedDbSnp dhcHumDerDenAncUtr5HighFreq dhcVcfDenisovaPinky dhcVcfDNK02 dhcVcfHGDP00456 dhcVcfHGDP00521 dhcVcfHGDP00542 dhcVcfHGDP00665 dhcVcfHGDP00778 dhcVcfHGDP00927 dhcVcfHGDP00998 dhcVcfHGDP01029 dhcVcfHGDP01284 dhcVcfHGDP01307 gtexEqtlCluster phastBiasTracts3 phastBiasPosteriors3 wgEncodeGencode2wayConsPseudo% wgEncodeGencodePolya% tablesIgnored mm9 allMm9RS_BW bamMmsNumtSSorted crgMapability% rest tablesIgnored mm10 cloneEnd% mm10Haplotypes mm10Patch4Haplotypes mm10Patch4Patches altSeqLiftOverPslP1 altSeqLiftOverPslP4 altSeqPatchesP1 wgEncodeGencode2wayConsPseudo% wgEncodeGencodePolya% tablesIgnored $ce chr%_wabaCbr wabaCbr nucleosomeControl nucleosomeFragmentsSense nucleosomeFragmentsAntisense nucleosomeStringency monoNucleosomesSense monoNucleosomesAntiSense nucleosomeControlSenseCoverage nucleosomeControlAntisenseCoverage nucleosomeAdjustedCoverage 25mersRepeats mt%Forward mt%Reverse wt%Forward wt%Reverse algBind% tablesIgnored $ci snapGene tablesIgnored $dm %_myp2a anophelesEcores bdtnpDnase% bdtnp%Fdr% fbGenscan fbGo fbRole fbUniProt mzD% refGenePfam tablesIgnored $galGal bgiCov ecoresTetraodon grcIncidentDb supercontig caCondor454 tablesIgnored $danRer grcIncidentDb phastConsElements wz_ests UMassInput UMassME1 UMassME1Hotspot UMassME1Peak UMassME3 UMassME3Hotspot UMassME3Peak tablesIgnored $canFam polyASeqSitesBrainFwd polyASeqSitesBrainRev polyASeqSitesKidneyFwd polyASeqSitesKidneyRev polyASeqSitesTestisFwd polyASeqSitesTestisRev mzH% tablesIgnored $anoGam anoEstNcl tablesIgnored $bosTau contigOrient tablesIgnored $apiMel brhInparalog modelRefGene scaffolds tablesIgnored $eboVir brTest geneDesc gire2014 gire2014FixedMissense gire2014KikwitMissense gire2014MayingaMissense gire2014Missense gire2014PolymorphicMissense gire2014SpecificSnps gireIntraHost gireZebov gireZebovMissense iedbBcell iedbBcellNeg iedbTcellI iedbTcellII mafSnp160way mafSnpStrainName160way muPIT newSequences newSequencesFrames newSequencesSnpView ncbiGenePfam pdb spMut testAllFrames testAllStrainFrames iedbPred% tablesIgnored $snpDb125 snp125ExceptionDesc tablesIgnored $snpDb126 snp126ExceptionDesc tablesIgnored $snpDb127 snp127ExceptionDesc tablesIgnored $hg acescan affyTranscriptome affyTxnPhase3FragsHDF affyTxnPhase3FragsHeLaCyto affyTxnPhase3FragsHeLaNuclear affyTxnPhase3FragsHepG2Cyto affyTxnPhase3FragsHepG2Nuclear affyTxnPhase3FragsJurkat affyTxnPhase3FragsNCCIT affyTxnPhase3FragsPC3 affyTxnPhase3FragsSK_N_AS affyTxnPhase3FragsU87MG affyTxnPhase3FragsHeLaTopStrand affyTxnPhase3FragsHeLaBottomStrand affyTxnPhase3FragsHepG2TopStrand affyTxnPhase3FragsHepG2BottomStrand affyTxnPhase3HDF affyTxnPhase3HeLaCyto affyTxnPhase3HeLaNuclear affyTxnPhase3HepG2Cyto affyTxnPhase3HepG2Nuclear affyTxnPhase3Jurkat affyTxnPhase3NCCIT affyTxnPhase3PC3 affyTxnPhase3SK_N_AS affyTxnPhase3U87MG affyTxnPhase3HeLabottom_strand affyTxnPhase3HeLatop_strand affyTxnPhase3HepG2bottom_strand affyTxnPhase3HepG2top_strand affyTxnPhase3HeLaBottomStrand affyTxnPhase3HeLaTopStrand affyTxnPhase3HepG2BottomStrand affyTxnPhase3HepG2TopStrand altLocations burgeRnaSeqGemMapper% chimpDels chimpParalogy chimpSimpleDiff celeraCoverage celeraDupPositive celeraOverlay cccTrendPvalBd cccTrendPvalCad cccTrendPvalCd cccTrendPvalHt cccTrendPvalRa cccTrendPvalT1d cccTrendPvalT2d ceuBcellRNASeqBW clinvarCnv clinvarMain cnpFosmid cnpIafrate cnpIafrate2 cnpLocke cnpRedon cnpSebat cnpSebat2 cnpSharp cnpSharp2 cnpSharpSampleCount cnpSharpSamples cnpTuzun cnvDevDelay% darned decodeFemale decodeFemaleCarrier decodeFemaleNonCarrier decodeHotSpotFemale decodeHotSpotMale decodeMale decodeMaleCarrier decodeMaleFemaleDifference decodeMaleNonCarrier decodeSexAveraged decodeSexAveragedCarrier decodeSexAveragedNonCarrier delConrad delConrad2 delHinds delHinds2 delMccarroll denisovaMethylation dgv% ecoresTetNig1 encode% eponine evsEsp6500 exaptedRepeats fox2ClipClusters fox2ClipSeq fox2ClipSeqDensityForwardStrand fox2ClipSeqDensityReverseStrand geneTests grcIncidentDb gwipsvizRiboseq haplotype hapMapRelease24CEURecombMap hapMapRelease24CombinedRecombMap hapMapRelease24YRIRecombMap hgdpGeo hgdpFst hgdpHzy% hgdpIhs% hgdpXpehh% hgmd hiSeqDepthTop% isca% laminB1 laminB1Lads lovd lrg mammalPsg neandertalMethylation nimhBipolarUs nimhBipolarDe ntHumChimpCodingDiff ntMito ntOoaHaplo ntSss% perlegen pg% polyaDb polyaPredict polyASeqSitesBrainFwd polyASeqSitesBrainRev polyASeqSitesKidneyFwd polyASeqSitesKidneyRev polyASeqSitesLiverFwd polyASeqSitesLiverRev polyASeqSitesMaqcBrain1Fwd polyASeqSitesMaqcBrain1Rev polyASeqSitesMaqcBrain2Fwd polyASeqSitesMaqcBrain2Rev polyASeqSitesMaqcUhr1Fwd polyASeqSitesMaqcUhr1Rev polyASeqSitesMaqcUhr2Fwd polyASeqSitesMaqcUhr2Rev polyASeqSitesMuscleFwd polyASeqSitesMuscleRev polyASeqSitesTestisFwd polyASeqSitesTestisRev promoterStanford pseudoYale recombRate sibGene sibTxGraph slamMouse slamNonCodingMouse slamRat slamNonCodingRat snp snp125ExceptionDesc snp126ExceptionDesc spMut switchDbTss syntenyMouse syntenyRat tajd% targetScanS tgpPhase1 tgpPhase1AccessibilityPilotCriteria tgpPhase1AccessibilityStrictCriteria tgpPhase3 ucsfChipSeqH3K4me3BrainCoverage ucsfMedipSeqBrainCoverage ucsfMedipSeqBrainCpG ucsfMreSeqBrainCpG ucsfRnaSeqBrainAllCoverage ucsfRnaSeqBrainSmartCoverage vistaEnhancers wgRna zoom1_affyTranscriptome zoom2_affyTranscriptome kiddEichlerValidAbc7 kiddEichlerValidAbc8 kiddEichlerValidAbc9 kiddEichlerValidAbc10 kiddEichlerValidAbc11 kiddEichlerValidAbc12 kiddEichlerValidAbc13 kiddEichlerValidAbc14 kiddEichlerValidG248 wgEncode% tablesIgnored $mm grcIncidentDb sibGene sibTxGraph syntenyRat syntenyHuman rikenCageCtssMinus rikenCageCtssPlus rikenCageTc broadStemChip% laminB1_AC laminB1_EF laminB1_ES laminB1_NP polyASeqSitesBrainFwd polyASeqSitesBrainRev polyASeqSitesKidneyFwd polyASeqSitesKidneyRev polyASeqSitesLiverFwd polyASeqSitesLiverRev polyASeqSitesMuscleFwd polyASeqSitesMuscleRev polyASeqSitesTestisFwd polyASeqSitesTestisRev wgEncodeGencodePolya% wgEncodeGencode2wayConsPseudo% tablesIgnored $ci tableList tablesIgnored $macFas tableList tablesIgnored $oreNil tableList tablesIgnored $panPan tableList tablesIgnored $panTro humanDels tablesIgnored $rheMac polyASeqSitesBrainFwd polyASeqSitesBrainRev polyASeqSitesIleumFwd polyASeqSitesIleumRev polyASeqSitesKidneyFwd polyASeqSitesKidneyRev polyASeqSitesLiverFwd polyASeqSitesLiverRev polyASeqSitesTestisFwd polyASeqSitesTestisRev tablesIgnored $rn all_sts_primer bactigPos ecores% polyASeqSitesBrainFwd polyASeqSitesBrainRev polyASeqSitesTestisFwd polyASeqSitesTestisRev recombRateRat syntenyMouse syntenyHuman tablesIgnored $sacCer 2micron_mrna 2micron_intronEst 2micron_est 2micron_gap sgdClone yeastP2P uwFootprintsMappability uwFootprintsPrints uwFootprintsTagCounts tablesIgnored $tetNig ecoresHg17 cytokines hoxGenes tablesIgnored $fr ecoresHg16 ecoresRn3 tablesIgnored hg16 chicken_hmrg rat_hmrg mouse_hmrg syntenyMm4 tablesIgnored anoGam3 ensemblGeneScaffold tablesIgnored canFam2 uncertified tablesIgnored susScr2 bosTau4ChainPileUp tablesIgnored calJac3 bacEnds bacEndCalJac3Singles tablesIgnored chrPic2 rmskBlastn tablesIgnored criGri1 rmskBlastn tableList tablesIgnored rheMac2 refSeqAnno tablesIgnored choHof1 tableList tablesIgnored dipOrd1 tableList tablesIgnored echTel2 tableList tablesIgnored echTel1 tableList tablesIgnored eriEur2 tableList tablesIgnored eriEur1 tableList tablesIgnored micMur2 tableList tablesIgnored micMur1 tableList tablesIgnored micOch1 tableList tablesIgnored ochPri2 tableList tablesIgnored ochPri3 tableList tablesIgnored papAnu2 tableList tablesIgnored papHam1 tableList tablesIgnored proCap1 tableList tablesIgnored pteVam1 tableList tablesIgnored sorAra2 tableList tablesIgnored sorAra1 tableList tablesIgnored staAur2 aaCountsALA aaCountsARG aaCountsASN aaCountsASP aaCountsCYS aaCountsGLN aaCountsGLU aaCountsGLY aaCountsHIS aaCountsILE aaCountsLEU aaCountsLYS aaCountsMET aaCountsNUL aaCountsPHE aaCountsPRO aaCountsSER aaCountsTER aaCountsTHR aaCountsTRP aaCountsTYR aaCountsUNK aaCountsVAL tablesIgnored tarSyr1 tableList tablesIgnored tarSyr2 tableList tablesIgnored tupBel1 tableList tablesIgnored tupChi1 tableList tablesIgnored vicPac1 tableList tablesIgnored vicPac2 tableList tablesIgnored $xenLae tableList tablesIgnored $xenTro tableList tablesIgnored hg18 phastBiasTracts3 phastBiasPosteriors3 phastBiasChimpTracts3 phastBiasChimpPosteriors3 tablesIgnored $tRNAsDbs tRNAs # Table types - only used in joinerGraph which is not part of the standard build and probably # doesn't work anymore. Probably not worth updating, but someone may want to resurrect # joinerGraph so here they are. type genePred $hg.acembly $gbd.ECgene $gbd.geneid $gbd.genscan $gbd.sgpGene $gbd.softberryGene $gbd.twinscan $gbd.ensGene $gbd.vegaGene $gbd.refGene $gbd.xenoRefGene $gbd.jgiFilteredModels $gbd.geneMapper type pepPred $hg.acemblyPep $gbd.ECgenePep $gbd.geneidPep $gbd.genscanPep $gbd.sgpPep $gbd.softberryPep $gbd.twinscanPep $gbd.ensPep $gbd.vegaPep $gbd.knownGenePep $ce.sangerPep dm1.bdgpGenePep $dm.flyBasePep type psl $hg.affyU95 $hg.affyU133 $hg.affyU133Plus2 $hg.HInvGeneMrna $mm.affyU74 $danRer.affyZebrafish $gbd.all_bacends $gbd.all_fosends $gbd.all_est $gbd.est $gbd.intronEst $gbd.xenoEst $gbd.xenoMrna $gbd.all_mrna $gbd.refSeqAli $gbd.all_sts_primer $gbd.all_sts_seq type estOrientInfo $gbd.estOrientInfo $gbd.mrnaOrientInfo type expRecord hgFixed.nci60Exps hgFixed.rosettaExps hgFixed.affyExps.id hgFixed.gnfHumanU95AllExps hgFixed.gnfHumanU95MedianExps hgFixed.gnfMouseU74aAllExps hgFixed.gnfMouseU74aMedianExps hgFixed.gnfMouseU74bAllExps hgFixed.gnfMouseU74bMedianExps hgFixed.gnfMouseU74cAllExps hgFixed.gnfMouseU74cMedianExps hgFixed.arbFlyLifeAllExps hgFixed.arbFlyLifeMedianExps hgFixed.kimWormLifeAllExps hgFixed.kimWormLifeMedianExps hgFixed.yeastChoCellCycleExps hgFixed.gladHumESExps type expData hgFixed.kimWormLifeAllRatio hgFixed.kimWormLifeMedianRatio hgFixed.gnfHumanU95All hgFixed.gnfHumanU95AllRatio hgFixed.gnfHumanU95Median hgFixed.gnfHumanU95MedianRatio hgFixed.gnfMouseU74aAll hgFixed.gnfMouseU74aAllRatio hgFixed.gnfMouseU74aMedian hgFixed.gnfMouseU74aMedianRatio hgFixed.gnfMouseU74bAll hgFixed.gnfMouseU74bAllRatio hgFixed.gnfMouseU74bMedian hgFixed.gnfMouseU74bMedianRatio hgFixed.gnfMouseU74cAll hgFixed.gnfMouseU74cAllRatio hgFixed.gnfMouseU74cMedian hgFixed.gnfMouseU74cMedianRatio hgFixed.arbFlyLifeAll hgFixed.arbFlyLifeAllRatio hgFixed.arbFlyLifeMedian hgFixed.arbFlyLifeMedianRatio hgFixed.kimWormLifeAllRatio hgFixed.kimWormLifeMedianRatio hgFixed.yeastChoCellCycle hgFixed.yeastChoCellCycleRatio hgFixed.gladHumES hgFixed.gladHumESRatio type exprBed $hg.affyRatio $mm.affyGnfU74A $mm.affyGnfU74B $mm.affyGnfU74C $hg.nci60 $rn.gnfAtlas2 # hgFixed.rosChr22Dat type expDistance $hg.gnfAtlas2Distance $hg.gnfU95Distance $mm.affyGnfU74ADistance $mm.affyGnfU74BDistance $mm.affyGnfU74CDistance $mm.mouseLandscapeDistance $hg.knownGnfDistance $ce.kimExpDistance $dm.arbExpDistance $sacCer.choExpDistance $hg.gladHumESDistance type chain $gbd.chr%_chain% $gbd.chr%_chainSelf type agpFrag $gbd.chr%_gold type agpGap $gbd.chr%_gap type gl $gbd.chr%_gl type knownTo $gbd.knownToCdsSnp $gbd.knownToEnsembl $gbd.knownToLocusLink $gbd.knownToPfam $gbd.knownToRefSeq $gbd.knownToAllenBrain $hg.knownToU95 $hg.knownToU133 $hg.knownToU133Plus2 $hg.knownToHInv $mm.knownToU74 $mm.knownToXM $ce.sangerToKim $ce.sangerToPfam $ce.sangerToRefSeq dm1.bdgpToLocusLink dm1.bdgpToPfam dm1.bdgpToRefSeq $sacCer.sgdToSwissProt $sacCer.sgdToSgd $sacCer.sgdToName type idName hgFixed.source hgFixed.organism hgFixed.library hgFixed.mrnaClone hgFixed.sex hgFixed.tissue hgFixed.development hgFixed.cell hgFixed.cds hgFixed.description hgFixed.author hgFixed.geneName hgFixed.productName hgFixed.keyword type blastTab $gbd.ceBlastTab $gbd.hgBlastTab $gbd.dmBlastTab $gbd.drBlastTab $gbd.mmBlastTab $gbd.rnBlastTab $gbd.scBlastTab $gbd.knownBlastTab $ce.sangerBlastTab dm1.bdgpBlastTab sacCer1.sgdBlastTab sacCer2.knownBlastTab type knownCanonical $gbd.knownCanonical $ce.sangerCanonical dm1.bdgpCanonical $sacCer.sgdCanonical type knownIsoforms $gbd.knownIsoforms $ce.sangerIsoforms dm1.bdgpIsoforms $sacCer.sgdIsoforms type rnaFold $gbd.foldUtr3 $gbd.foldUtr5 type bed $gbd.vegaPseudoGene $sacCer.sgdOther type geneAndProt $kgDb.knownGene $ce.sangerGene dm1.bdgpGene $sacCer.sgdGene