22f0c874d90f86f1bfa4014ee29f9c0ee0bff517 markd Tue Jun 25 23:17:29 2019 -0700 load transMap V5 diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index dd19aa8..fdb28af 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -188,36 +188,30 @@ # 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 transMap databases -# transMapDb not public: dasNov1,echTel1,echTel2,loxAfr1,oryCun1,otoGar1,loxAfr3 -set transMapDb anoCar1,anoCar2,bosTau4,calJac1,calJac3,canFam2,cavPor3,chlSab2,choHof1,danRer5,danRer6,echTel1,echTel2,equCab2,eriEur1,eriEur2,felCat3,felCat8,fr2,fr3,gadMor1,galGal3,gasAcu1,hg18,hg19,hg38,loxAfr3,macFas5,melUnd1,micMur1,micOch1,mm9,mm10,monDom4,monDom5,ochPri2,ochPri3,oreNil2,ornAna1,oryCun2,oryLat2,panPan1,panTro2,panTro4,papAnu2,papHam1,petMar1,ponAbe2,proCap1,pteVam1,rheMac2,rn4,saiBol1,sorAra1,sorAra2,speTri2,taeGut1,tarSyr1,tarSyr2,tetNig1,tetNig2,tupBel1,tupChi1,turTru2,vicPac1,vicPac2,xenTro2,xenTro3,xenTro7 - -set transMapDbV3 ailMel1,allMis1,allSin1,amaVit1,anaPla1,anoCar2,apaSpi1,araMac1,astMex1,bosTau8,calJac3,camFer1,canFam3,capHir1,cavPor3,cerSim1,cheMyd1,chiLan1,chlSab2,choHof1,chrAsi1,colLiv1,conCri1,criGri1,danRer7,dasNov3,dipOrd1,echTel2,eleEdw1,eptFus1,equCab2,eriEur2,falChe1,falPer1,felCat5,felCat8,ficAlb2,fr3,gadMor1,galGal4,gasAcu1,geoFor1,gorGor3,hapBur1,hetGla2,hg19,hg38,jacJac1,latCha1,lepOcu1,lepWed1,letCam1,lipVex1,loxAfr3,macEug2,macFas5,mayZeb1,melGal1,melGal5,melUnd1,mesAur1,micMur1,micOch1,mm10,mm9,monDom5,musFur1,myoDav1,myoLuc2,neoBri1,nomLeu3,ochPri3,octDeg1,odoRosDiv1,orcOrc1,oreNil2,ornAna1,oryAfe1,oryCun2,oryLat2,otoGar3,oviAri3,panHod1,panPan1,panTig1,panTro4,papAnu2,pelSin1,petMar2,phyCat1,ponAbe2,proCap1,pseHum1,pteAle1,pteVam1,punNye1,rn5,saiBol1,sarHar1,sorAra2,speTri2,susScr3,taeGut2,takFla1,tarSyr2,tetNig2,triMan1,tupBel1,tupChi1,tupChi1,turTru2,vicPac2,xenTro7,xipMac1,zonAlb1 - # 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,RhiRox1,Rn3,Rn4,Rn5,Rn6,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) @@ -7099,300 +7093,30 @@ 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 -#### -# transmap V2 (tables not versioned) -## -# transMap alignment (psl) tables and info tables; 1-to-1 mapping -identifier transMapAlnInfoRefSeqId -"transMap RefSeq per-genome alignments" - $transMapDb.transMapAlnRefSeq.qName unique - $transMapDb.transMapInfoRefSeq.mappedId unique full - -identifier transMapAlnInfoUcscGenesId -"transMap UcscGenes per-genome alignments" - $transMapDb.transMapAlnUcscGenes.qName unique - $transMapDb.transMapInfoUcscGenes.mappedId unique full - -identifier transMapAlnInfoMRnaId -"transMap MRna per-genome alignments" - $transMapDb.transMapAlnMRna.qName unique - $transMapDb.transMapInfoMRna.mappedId unique full - -identifier transMapAlnInfoSplicedEstId -"transMap SplicedEst per-genome alignments" - $transMapDb.transMapAlnSplicedEst.qName unique - $transMapDb.transMapInfoSplicedEst.mappedId unique full - -# transMap info table and hgFixed src tables -identifier transMapSrcInfoRefSeqId -"transMap RefSeq pre-geneome alignment to source" - hgFixed.transMapSrcRefSeq.id dupeOk - $transMapDb.transMapInfoRefSeq.srcId - -identifier transMapSrcInfoUcscGenesId -"transMap UcscGenes pre-geneome alignment to source" - hgFixed.transMapSrcUcscGenes.id dupeOk - $transMapDb.transMapInfoUcscGenes.srcId - -identifier transMapSrcInfoMRnaId -"transMap MRna pre-geneome alignment to source" - hgFixed.transMapSrcMRna.id dupeOk - $transMapDb.transMapInfoMRna.srcId - -identifier transMapSrcInfoSplicedEstId -"transMap SplicedEst pre-geneome alignment to source" - hgFixed.transMapSrcSplicedEst.id dupeOk - $transMapDb.transMapInfoSplicedEst.srcId - -# transMap aln table and hgFixed src tables -identifier transMapSrcAlnUcscGenesId -"transMap UcscGenes alignment to source" - hgFixed.transMapSrcUcscGenes.id dupeOk chopAfter=- - $transMapDb.transMapAlnUcscGenes.qName chopAfter=- - -identifier transMapSrcAlnMRnaId -"transMap MRnas alignment to source" - hgFixed.transMapSrcMRna.id dupeOk chopAfter=- - $transMapDb.transMapAlnMRna.qName chopAfter=- - -identifier transMapSrcAlnRefSeqId -"transMap RefSeqs alignment to source" - hgFixed.transMapSrcRefSeq.id dupeOk chopAfter=- - $transMapDb.transMapAlnRefSeq.qName chopAfter=- - -identifier transMapSrcAlnSplicedEstId -"transMap SplicedEsts alignment to source" - hgFixed.transMapSrcSplicedEst.id dupeOk chopAfter=- - $transMapDb.transMapAlnSplicedEst.qName chopAfter=- - -# transMap source tables -identifier transMapSrcRefSeqId -"transMap RefSeq source gene and sequences " - hgFixed.transMapSrcRefSeq.id dupeOk chopAfter=- - hgFixed.transMapSeqRefSeq.acc - hgFixed.transMapGeneRefSeq.id - -identifier transMapSrcUcscGenesId -"transMap UcscGenes source gene and sequences " - hgFixed.transMapSrcUcscGenes.id dupeOk chopAfter=- - hgFixed.transMapSeqUcscGenes.acc - hgFixed.transMapGeneUcscGenes.id - -identifier transMapSrcMRnaId -"transMap MRna source gene and sequences " - hgFixed.transMapSrcMRna.id dupeOk chopAfter=- - hgFixed.transMapSeqMRna.acc - hgFixed.transMapGeneMRna.id - -identifier transMapSrcSplicedEstId -"transMap SplicedEst source sequences " - hgFixed.transMapSrcSplicedEst.id dupeOk chopAfter=- - hgFixed.transMapSeqSplicedEst.acc - -# transMap extFile tables -identifier transMapExtFileRefSeqId -"transMap RefSeq external file " - hgFixed.transMapSeqRefSeq.extFile dupeOk - hgFixed.transMapExtFileRefSeq.id unique - -identifier transMapExtFileUcscGenesId -"transMap UcscGenes external file " - hgFixed.transMapSeqUcscGenes.extFile dupeOk - hgFixed.transMapExtFileUcscGenes.id unique - -identifier transMapExtFileMRnaId -"transMap MRna external file " - hgFixed.transMapSeqMRna.extFile dupeOk - hgFixed.transMapExtFileMRna.id unique - -identifier transMapExtFileSplicedEstId -"transMap SplicedEst external file " - hgFixed.transMapSeqSplicedEst.extFile dupeOk - hgFixed.transMapExtFileSplicedEst.id unique - -# transMap and knownGenes -identifier transMapGeneUcscGenesId fuzzy -"UCSC Genes and transMapGene table" - hgFixed.transMapGeneUcscGenes.id - $kgDb3.knownGene.name - -identifier transMapAlnKnownGeneHgId -"UCSC Genes and transMapAln table" - mm9.knownGene.name - hg18.transMapAlnUcscGenes.qName chopAfter=- - -identifier transMapAlnKnownGeneMmId -"UCSC Genes and transMapAln table" - hg19.knownGene.name - mm9.transMapAlnUcscGenes.qName chopAfter=- - -# end transmap V2 -### - -#### -# transmap V3 -## -# transMap alignment (psl) tables and info tables; 1-to-1 mapping -identifier transMapAlnInfoEnsemblV3Id -"transMap GENCODE/Ensembl per-genome alignments" - $transMapDb.transMapAlnEnsemblV3.qName unique - $transMapDb.transMapInfoEnsemblV3.mappedId unique full - -identifier transMapAlnInfoRefSeqV3Id -"transMap RefSeq per-genome alignments" - $transMapDb.transMapAlnRefSeqV3.qName unique - $transMapDb.transMapInfoRefSeqV3.mappedId unique full - -identifier transMapAlnInfoUcscGenesV3Id -"transMap UcscGenes per-genome alignments" - $transMapDb.transMapAlnUcscGenesV3.qName unique - $transMapDb.transMapInfoUcscGenesV3.mappedId unique full - -identifier transMapAlnInfoMRnaV3Id -"transMap MRna per-genome alignments" - $transMapDb.transMapAlnMRnaV3.qName unique - $transMapDb.transMapInfoMRnaV3.mappedId unique full - -identifier transMapAlnInfoSplicedEstV3Id -"transMap SplicedEst per-genome alignments" - $transMapDb.transMapAlnSplicedEstV3.qName unique - $transMapDb.transMapInfoSplicedEstV3.mappedId unique full - -# transMap info table and hgFixed src tables -identifier transMapSrcInfoEnsemblV3Id -"transMap Ensembl pre-geneome alignment to source" - hgFixed.transMapSrcEnsemblV3.id dupeOk - $transMapDb.transMapInfoEnsemblV3.srcId - -identifier transMapSrcInfoRefSeqV3Id -"transMap RefSeq pre-geneome alignment to source" - hgFixed.transMapSrcRefSeqV3.id dupeOk - $transMapDb.transMapInfoRefSeqV3.srcId - -identifier transMapSrcInfoUcscGenesV3Id -"transMap UcscGenes pre-geneome alignment to source" - hgFixed.transMapSrcUcscGenesV3.id dupeOk - $transMapDb.transMapInfoUcscGenesV3.srcId - -identifier transMapSrcInfoMRnaV3Id -"transMap MRna pre-geneome alignment to source" - hgFixed.transMapSrcMRnaV3.id dupeOk - $transMapDb.transMapInfoMRnaV3.srcId - -identifier transMapSrcInfoSplicedEstV3Id -"transMap SplicedEst pre-geneome alignment to source" - hgFixed.transMapSrcSplicedEstV3.id dupeOk - $transMapDb.transMapInfoSplicedEstV3.srcId - -# transMap aln table and hgFixed src tables -identifier transMapSrcAlnUcscGenesV3Id -"transMap UcscGenes alignment to source" - hgFixed.transMapSrcUcscGenesV3.id dupeOk chopAfter=- - $transMapDb.transMapAlnUcscGenesV3.qName chopAfter=- - -identifier transMapSrcAlnMRnaV3Id -"transMap MRnas alignment to source" - hgFixed.transMapSrcMRnaV3.id dupeOk chopAfter=- - $transMapDb.transMapAlnMRnaV3.qName chopAfter=- - -identifier transMapSrcAlnEnsemblV3Id -"transMap Ensembl alignment to source" - hgFixed.transMapSrcEnsemblV3.id dupeOk chopAfter=- - $transMapDb.transMapAlnEnsemblV3.qName chopAfter=- - -identifier transMapSrcAlnRefSeqV3Id -"transMap RefSeq alignment to source" - hgFixed.transMapSrcRefSeqV3.id dupeOk chopAfter=- - $transMapDb.transMapAlnRefSeqV3.qName chopAfter=- - -identifier transMapSrcAlnSplicedEstV3Id -"transMap SplicedEsts alignment to source" - hgFixed.transMapSrcSplicedEstV3.id dupeOk chopAfter=- - $transMapDb.transMapAlnSplicedEstV3.qName chopAfter=- - -# transMap source tables -identifier transMapSrcEnsemblV3Id -"transMap Ensembl source gene and sequences " - hgFixed.transMapSrcEnsemblV3.id dupeOk chopAfter=- - hgFixed.transMapSeqEnsemblV3.acc - hgFixed.transMapGeneEnsemblV3.id - -identifier transMapSrcRefSeqV3Id -"transMap RefSeq source gene and sequences " - hgFixed.transMapSrcRefSeqV3.id dupeOk chopAfter=- - hgFixed.transMapSeqRefSeqV3.acc - hgFixed.transMapGeneRefSeqV3.id - -identifier transMapSrcUcscGenesV3Id -"transMap UcscGenes source gene and sequences " - hgFixed.transMapSrcUcscGenesV3.id dupeOk chopAfter=- - hgFixed.transMapSeqUcscGenesV3.acc - hgFixed.transMapGeneUcscGenesV3.id - -identifier transMapSrcMRnaV3Id -"transMap MRna source gene and sequences " - hgFixed.transMapSrcMRnaV3.id dupeOk chopAfter=- - hgFixed.transMapSeqMRnaV3.acc - hgFixed.transMapGeneMRnaV3.id - -identifier transMapSrcSplicedEstV3Id -"transMap SplicedEst source sequences " - hgFixed.transMapSrcSplicedEstV3.id dupeOk chopAfter=- - hgFixed.transMapSeqSplicedEstV3.acc - -# transMap extFile tables -identifier transMapExtFileEnsemblV3Id -"transMap Ensembl external file " - hgFixed.transMapSeqEnsemblV3.extFile dupeOk - hgFixed.transMapExtFileEnsemblV3.id unique - -identifier transMapExtFileRefSeqV3Id -"transMap RefSeq external file " - hgFixed.transMapSeqRefSeqV3.extFile dupeOk - hgFixed.transMapExtFileRefSeqV3.id unique - -identifier transMapExtFileUcscGenesV3Id -"transMap UcscGenes external file " - hgFixed.transMapSeqUcscGenesV3.extFile dupeOk - hgFixed.transMapExtFileUcscGenesV3.id unique - -identifier transMapExtFileMRnaV3Id -"transMap MRna external file " - hgFixed.transMapSeqMRnaV3.extFile dupeOk - hgFixed.transMapExtFileMRnaV3.id unique - -identifier transMapExtFileSplicedEstV3Id -"transMap SplicedEst external file " - hgFixed.transMapSeqSplicedEstV3.extFile dupeOk - hgFixed.transMapExtFileSplicedEstV3.id unique - -# end transmap V3 -### - 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 @@ -7721,34 +7445,30 @@ $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 - $transMapDb.transMapAlnUcscGenes - $transMapDb.transMapAlnRefSeq - $transMapDb.transMapAlnMRna - $transMapDb.transMapAlnSplicedEst 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 @@ -7893,48 +7613,30 @@ type rnaFold $gbd.foldUtr3 $gbd.foldUtr5 type bed $gbd.vegaPseudoGene $sacCer.sgdOther type geneAndProt $kgDb.knownGene $ce.sangerGene dm1.bdgpGene $sacCer.sgdGene -type transMapInfo - $transMapDb.transMapInfoRefSeq - $transMapDb.transMapInfoUcscGenes - $transMapDb.transMapInfoMRna - $transMapDb.transMapInfoSplicedEst - -type transMapSrc - hgFixed.transMapSrcRefSeq - hgFixed.transMapSrcUcscGenes - hgFixed.transMapSrcMRna - hgFixed.transMapSrcSplicedEst - -type transMapGene - hgFixed.transMapGeneRefSeq - hgFixed.transMapGeneUcscGenes - hgFixed.transMapGeneMRna - - # 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