9c70d91534dd8366a57c563718c715308d3dac78 gperez2 Mon Jun 21 16:03:47 2021 -0700 Code review edits, shorting longLabel’s within 80 characters, refs #27743 diff --git src/hg/makeDb/trackDb/human/hg38/trackDb.ra src/hg/makeDb/trackDb/human/hg38/trackDb.ra index 4f02dc1..8319028 100644 --- src/hg/makeDb/trackDb/human/hg38/trackDb.ra +++ src/hg/makeDb/trackDb/human/hg38/trackDb.ra @@ -1,848 +1,848 @@ include ../../refSeqComposite.ra include barCharts.ra include hoffMap.ra include cancerExpr.ra include mane.ra include gdcCancer.ra include cortexVelmeshev.ra include heartCellAtlas.ra include kidneyStewart.ra include muscleDeMicheli.ra #include lungVieiraBraga.ra include fetalGeneAtlas.ra include bloodHao.ra include lungTravaglini2020.ra include skinSoleBoldo.ra include liverMacParland.ra include pancreasBaron.ra include ileumWang.ra include colonWang.ra include rectumWang.ra include placentaVentoTormo.ra include singleCellMerged.ra #include lungMadissoon.ra include liftOver.ra include exomeProbesets.ra track miRnaAtlas compositeTrack on shortLabel miRNA Tissue Atlas longLabel Tissue-Specific microRNA Expression from Two Individuals type bigBarChart group expression maxLimit 52000 barChartLabel Tissue configurable off subGroup1 view View a_A=Sample1 b_B=Sample2 track miRnaAtlasSample1 type bigBarChart visibility pack parent miRnaAtlas view a_A configurable on track miRnaAtlasSample1BarChart url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$ url2Label miRBase v21 Precursor Accession: parent miRnaAtlasSample1 visibility full shortLabel Sample 1 longLabel miRNA Tissue Atlas microRna Expression bigDataUrl /gbdb/hg38/bbi/miRnaAtlasSample1.bb barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample1Matrix.txt barChartSampleUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample1.txt barChartBars adipocyte artery colon dura_mater kidney liver lung muscle myocardium skin \ spleen stomach testis thyroid small_intestine bone gallbladder fascia bladder epididymis \ tunica_albuginea nerve_nervus_intercostalis arachnoid_mater brain barChartColors #F7A028 #F73528 #DEBE98 #86BF80 #CDB79E #CDB79E #9ACD32 #7A67AE #9745AC #1E90FF \ \#CDB79E #FFD39B #A6A6A6 #008B45 #CDB79E #BD34D7 #CDA7FE #4C7CD7 #CBD79E #A6F6A1 \ \#A6CEA4 #FFD700 #86BF10 #EEEE00 group expression maxLimit 52000 barChartLabel Tissue barChartUnit Quantile_Normalized_Expression html miRnaAtlas configurable on subGroups view=a_A searchIndex name track miRnaAtlasSample2 type bigBarChart visibility pack parent miRnaAtlas view b_B configurable on track miRnaAtlasSample2BarChart url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$ url2Label miRBase v21 Precursor Accession: parent miRnaAtlasSample2 visibility full shortLabel Sample 2 longLabel miRNA Tissue Atlas microRna Expression bigDataUrl /gbdb/hg38/bbi/miRnaAtlasSample2.bb barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample2Matrix.txt barChartSampleUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample2.txt barChartBars adipocyte artery colon dura_mater kidney liver lung muscle myocardium skin \ spleen stomach testis thyroid small_intestine_duodenum small_intestine_jejunum pancreas \ kidney_glandula_suprarenalis kidney_cortex_renalis kidney_medulla_renalis esophagus prostate \ bone_marrow vein lymph_node nerve_not_specified pleura brain_pituitary_gland spinal_cord \ brain_thalamus brain_white_matter brain_nucleus_caudatus brain_gray_matter \ brain_cerebral_cortex_temporal brain_cerebral_cortex_frontal \ brain_cerebral_cortex_occipital brain_cerebellum barChartColors #F7A028 #F73528 #DEBE98 #86BF80 #CDB79E #CDB79E #9ACD32 #7A67AE #9745AC #1E90FF \ \#CDB79E #FFD39B #A6A6A6 #008B45 #CDB79E #CDB79E #CD9B1D \ \#CDB79E #CDB79E #CDB79E #AC8F69 #D9D9D9 #BD3487 \ \#FF00FF #EE82EE #F7E300 #73A585 #B4EEB4 #EEEE00 \ \#EEEE00 #EEEE00 #EEEE00 #EEEE00 \ \#EEEE00 #EEEE00 \ \#EEEE00 #EEEE00 group expression maxLimit 52000 barChartLabel Tissue barChartUnit Quantile_Norm_Expr html miRnaAtlas configurable on subGroups view=b_B searchIndex name searchTable miRnaAtlasSample1BarChart searchType bigBed searchPriority 1 searchDescription miRNA Tissue Atlas Sample 1 searchMethod exact semiShortCircuit 1 searchTable miRnaAtlasSample2BarChart searchType bigBed searchPriority 1 searchDescription miRNA Tissue Atlas Sample 2 searchMethod exact semiShortCircuit 1 track cosmicRegions shortLabel COSMIC Regions longLabel Catalogue of Somatic Mutations in Cancer V82 type bigBed 8 + bigDataUrl /gbdb/hg38/cosmic/cosMutHg38V82.bb labelFields cosmLabel group phenDis color 200, 0, 0 url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$$ urlLabel COSMIC ID: searchIndex name,cosmLabel tableBrowser off mouseOverField _mouseOver html cosmicRegions noScoreFilter on searchTable cosmicRegions searchPriority 2.07207 searchType bigBed searchDescription COSMIC Regions track coriellDelDup override origAssembly hg19 pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19" track revel override origAssembly hg19 pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19" include nonCodingRNAs.ra #track wgRna override #dataVersion miRBase Release 15.0 (April 2010) and snoRNABase Version 3 #pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19" track hgIkmc override origAssembly hg19 pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19" track fishClones override origAssembly hg18 pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18" track fosEndPairs override origAssembly hg18 pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18" track interactions override directUrl hgGeneGraph?db=hg38&gene=%s track par override group x visibility hide track windowmaskerSdust override group rep priority 8 pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track nestedRepeats override group rep priority 2 track simpleRepeat override group rep priority 7 pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track rmskJoinedBaseline override group rep priority 4 visibility hide track stsMap override visibility hide searchName assemblyAcc searchTable gold searchMethod prefix query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 5 shortCircuit 1 termRegex [A-Z][A-Z0-9]+(\.[0-9]+)? # Local declaration so that local gap.html is picked up. track gap override html gap visibility hide pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" include rmskTracks.ra track ctgPos2 shortLabel GRC Contigs longLabel Genome Reference Consortium Contigs group map visibility hide type ctgPos url https://www.ncbi.nlm.nih.gov/nuccore/$$ chromosomes chr1,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chrX,chrY searchTable ctgPos2 searchMethod prefix shortCircuit 1 termRegex [GK][LI][028][0-9]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,contig from %s where contig like '%s%%' searchPriority 5 track scaffolds shortLabel Scaffolds longLabel GRCh38 Defined Scaffold Identifiers group map visibility hide color 0,0,0 type bed 4 . searchTable scaffolds searchMethod prefix searchType bed shortCircuit 1 termRegex [1-9HMXY][0-9A-Z_]* searchPriority 18 track analysisGap shortLabel Analysis Gap longLabel Extra Gap Locations in Analysis Set Sequence on chr5, 14, 19, 21, 22, Y group x visibility hide type bed 4 . chromosomes chr14,chr19,chr21,chr22,chr5,chrY track hg38ContigDiff shortLabel Hg19 Diff longLabel Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19) visibility hide group map type bed 9 . scoreFilterByRange on itemRgb on color 0,0,0 urlLabel Genbank accession: url https://www.ncbi.nlm.nih.gov/nuccore/$$ track centromeres shortLabel Centromeres longLabel Centromere Locations group map visibility hide type bed 4 . chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY color 255,0,0 url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI accession record: include ../chainNetPrimate.ra include ../chainNetPlacental.ra include ../chainNetVertebrate.ra track contigAlignmentSegments shortLabel ContigSegments longLabel Non-bridged Contig Segments Used in lastz/chain/net Alignment Pipeline group x visibility hide type bed 4 track chainSelf override longLabel $Organism Chained Self Alignments group rep priority 6 chainColor Normalized Score matrixHeader A, C, G, T matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 type chain hg38 otherDb hg38 chainNormScoreAvailable yes scoreFilter 20000 track multiz4way shortLabel Cons 4-way longLabel 4-Way Multiz Alignment & Conservation group compGeno visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 # wiggle phastCons4way # spanList 1 pairwiseHeight 12 yLineOnOff Off # frames multiz4wayFrames # irows on autoScale Off windowingFunction mean summary multiz4waySummary speciesCodonDefault hg38 speciesGroups mammal sGroup_mammal rheMac3 mm10 canFam3 treeImage phylo/hg38_4way.gif include defaultPriority.ra track altSeqLiftOverBigPsl #superTrack altSequence pack visibility hide shortLabel Big Alt Map longLabel Big GRCh38 Alignments to the Alternate Sequences/Haplotypes type bigPsl bigDataUrl http://hgwdev.soe.ucsc.edu/~braney/altSeqLiftOverPsl.bb html altSequence indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffBases baseColorUseSequence lfExtra #baseColorUseSequence extFile seqNcbiAltSequence extNcbiAltSequence release alpha track altSequenceExp superTrack on shortLabel Exp Alt Map longLabel GRCh38 Haplotype to Reference Sequence Mapping Correspondence visibility hide group x track ncbiAltMappingsChain superTrack altSequenceExp pack shortLabel Alt Map Chain longLabel Chain Mappings to the Alternate Sequences/Haplotypes type chain hg38 spectrum on html altSequence track ncbiAltMappingsMaf superTrack altSequenceExp pack shortLabel Alt Map Maf longLabel Maf Mappings to the Alternate Sequences/Haplotypes type maf html altSequence include trackDb.4way.ra alpha include trackDb.5way.ra alpha include trackDb.7way.ra alpha include trackDb.17way.ra alpha include trackDb.20way.ra alpha include trackDb.27way.ra alpha include trackDb.30way.ra include trackDb.10way.ra include trackDb.mito204way.ra track ucscRetroAli8 shortLabel Retroposed Genes 8.0 longLabel Retroposed Genes V8, Including Pseudogenes group genes type psl color 20,0,250 visibility hide ucscRetroInfo ucscRetroInfo8 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds8 baseColorUseSequence extFile ucscRetroSeq8 ucscRetroExtFile8 indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 searchName ucscRetroInfoRefSeq8 searchTable ucscRetroAli8 searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo8 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo8.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 track mrnaBig bigDataUrl http://hgwdev.soe.ucsc.edu/~braney/bigMrna.bb shortLabel Big $Organism mRNAs longLabel Big $Organism mRNAs from GenBank group x visibility hide type bigPsl baseColorUseCds given #baseColorUseSequence genbank baseColorUseSequence lfExtra baseColorDefault diffCodons #baseColorDefault diffBases showDiffBasesAllScales . indelDoubleInsert on indelQueryInsert on indelPolyA on release alpha searchName ucscRetroInfoMrna8 searchTable ucscRetroAli8 searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt8 searchTable ucscRetroAli8 searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo8 xrefQuery select ucscRetroInfo8.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene8 searchTable ucscRetroAli8 searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo8 xrefQuery select ucscRetroInfo8.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track ucscRetroAli9 shortLabel RetroGenes V9 longLabel Retroposed Genes V9, Including Pseudogenes group genes type psl color 20,0,250 visibility hide ucscRetroInfo ucscRetroInfo9 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds9 baseColorUseSequence extFile ucscRetroSeq9 ucscRetroExtFile9 indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 dataVersion Jan. 2015 exonNumbers off searchName ucscRetroInfoRefSeq9 searchTable ucscRetroAli9 searchDescription Retroposed Genes V9, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo9 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo9.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 searchName ucscRetroInfoMrna9 searchTable ucscRetroAli9 searchDescription Retroposed Genes V9, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt9 searchTable ucscRetroAli9 searchDescription Retroposed Genes V9, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo9 xrefQuery select ucscRetroInfo9.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene9 searchTable ucscRetroAli9 searchDescription Retroposed Genes V9, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo9 xrefQuery select ucscRetroInfo9.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track tgpPhase3 shortLabel 1000G Ph3 Vars longLabel 1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels type vcfTabix group varRep visibility hide maxWindowToDraw 5000000 showHardyWeinberg on geneTrack ncbiRefSeqCurated chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX track tgpTrios type vcfPhasedTrio group varRep chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX maxWindowToDraw 5000000 shortLabel 1000 Genomes Trios longLabel Thousand Genomes Project Family VCF Trios vcfUseAltSampleNames on vcfDoFilter off vcfDoQual off vcfDoMaf off compositeTrack on geneTrack ncbiRefSeqCurated track tgpNA19685_m011_MXL parent tgpTrios type vcfPhasedTrio shortLabel m011 MXL Trio longLabel 1000 Genomes m011 Mexican Ancestry from Los Angeles Trio vcfChildSample NA19685|child vcfParentSamples NA19660|mother,NA19661|father visibility full track tgpNA19675_m004_MXL parent tgpTrios type vcfPhasedTrio shortLabel m004 MXL Trio longLabel 1000 Genomes m004 Mexican Ancestry from Los Angeles Trio vcfChildSample NA19675|child vcfParentSamples NA19678|mother,NA19679|father visibility full track tgpNA19240_Y117_YRI parent tgpTrios type vcfPhasedTrio shortLabel Y117 YRI Trio longLabel 1000 Genomes Yoruban in Ibadan, Nigeria Trio vcfChildSample NA19240|child vcfParentSamples NA19238|mother,NA19239|father visibility full track tgpNA12878_1463_CEU parent tgpTrios type vcfPhasedTrio shortLabel 1463 CEU Trio longLabel 1000 Genomes Utah CEPH Trio vcfChildSample NA12878|child vcfParentSamples NA12892|mother,NA12891|father visibility full track tgpHG02024_VN049_KHV parent tgpTrios type vcfPhasedTrio shortLabel VN049 KHV Trio longLabel 1000 Genomes Kinh in Ho Chi Minh City, Vietnam Trio vcfChildSample HG02024|child vcfParentSamples HG02025|mother,HG02026|father visibility full track tgpHG00733_PR05_PUR parent tgpTrios type vcfPhasedTrio shortLabel PR05 PUR Trio longLabel 1000 Genomes Puerto Ricans from Puerto Rico Trio vcfChildSample HG00733|child vcfParentSamples HG00732|mother,HG00731|father visibility full track tgpHG00702_SH089_CHS parent tgpTrios type vcfPhasedTrio shortLabel SH089 CHS Trio longLabel 1000 Genomes Southern Han Chinese Trio vcfChildSample HG00702|child vcfParentSamples HG00657|mother,HG00656|father visibility full track genomicSuperDups override group rep priority 5 track sibGene override url http://ccg.vital-it.ch/cgi-bin/tromer/tromer_quick_search_internal.pl?db=hg38&query_str=$$ urlLabel SIB link: track sibTxGraph override url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?db=hg38&species=H.+sapiens&tromer=$$ track altSeqLiftOverPsl override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track fixSeqLiftOverPsl override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track gtexGene override pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"; p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track cpgIslandSuper override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track est override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track xenoMrna override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track xenoEst override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track augustusGene override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track genscan override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track ucscGenePfam override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track orfeomeMrna override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track mgcFullMrna override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track xenoRefGene override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track knownAlt override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track cytoBand override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track gc5BaseBw override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track ucscToRefSeq override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" track ucscToINSDC override pennantIcon p12 black http://genome.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p12 patch sequences" include trackDb.cloneEnd.ra include hg38Patch11.ra alpha include knownGene.ra include trackDb.100way.ra include trackDb.145way.ra alpha include trackDb.241way.ra alpha,beta include trackDb.241wayBM.ra alpha # track multiz145way # shortLabel 145way maf # longLabel 145-way MAF track # group compGeno # visibility hide # type maf track microsat override group rep priority 3 searchTable sgpGene searchType genePred termRegex chr[0-9MUXYn]+[BGHIJKLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)? searchPriority 50 searchTable geneid searchType genePred searchMethod prefix termRegex chr[0-9MUXYn]+[BGHIJKLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)? searchPriority 50 track gwasCatalog override snpTable snp144 snpVersion 144 # override to use hg38 specific html page track crispr override html crispr track ncbiRefSeqRefGene compositeTrack on shortLabel refGeneRefSeq longLabel comparing gene tracks refGene with ncbiRefSeq visibility hide type bed 12 group x track lostRefGene subTrack ncbiRefSeqRefGene shortLabel lostRefGene longLabel refGene predictions 'lost' in NCBI RefSeq track color 155,0,0 track exactRefGene subTrack ncbiRefSeqRefGene shortLabel exactRefGene longLabel refGene predictions 'exact' in NCBI RefSeq track color 0,155,0 track compatibleRefGene subTrack ncbiRefSeqRefGene shortLabel compatibleRefGene longLabel refGene predictions 'compatible' in NCBI RefSeq track color 0,0,255 track gtexBrain release alpha type barChart maxLimit 370000 barChartUnit RPKM barChartLabel Brain Regions barChartMetric median barChartBars \ brainAmygdala brainAnCinCortex brainCaudate brainCerebelHemi brainCerebellum brainCortex \ brainFrontCortex brainHippocampus brainHypothalamus brainNucAccumbens brainPutamen \ brainSpinalcord brainSubstanNigra bedNameLabel Gene accession shortLabel GTEx Brain longLabel GTEx Brain Gene Expression in barChart track format group expression track dgvPlus override group varRep track dgvMerged override parent dgvPlus on type bigBed 9 + bigDataUrl /gbdb/hg38/dgv/dgvMerged.bb filter._size 1:9734324 filterByRange._size on filterLabel._size Genomic size of variant filterValues.varType complex,deletion,duplication,gain,gain+loss,insertion,inversion,loss,mobile element insertion,novel sequence insertion,sequence alteration,tandem duplication track dgvSupporting override parent dgvPlus type bigBed 9 + bigDataUrl /gbdb/hg38/dgv/dgvSupporting.bb filter._size 1:9320633 filterByRange._size on filterLabel._size Genomic size of variant filterValues.varType complex,deletion,duplication,gain,gain+loss,insertion,inversion,loss,mobile element insertion,novel sequence insertion,sequence alteration,tandem duplication track gtexTranscExpr override bigDataUrl /gbdb/hg38/gtex/gtexTranscExpr.bb # ENCODE tracks include trackDb.gencode.ra include wgEncodeReg.ra include encode3.ra include wgEncodeReg.dev.ra alpha include hic.ra include gnomad.ra beta,public include gnomad.alpha.ra alpha include platinumGenomes.ra track epdNew compositeTrack on shortLabel EPDnew Promoters longLabel Promoters from EPDnew html ../../epdNewPromoter type bigBed 8 group expression visibility hide urlLabel EPDnew link: bedNameLabel Promoter ID exonArrows on track epdNewPromoter shortLabel EPDnew v6 longLabel Promoters from EPDnew human version 006 parent epdNew on bigDataUrl /gbdb/$D/bbi/epdNewHuman006.$D.bb dataVersion EPDNew Human Version 006 (May 2018) url https://epd.epfl.ch/cgi-bin/get_doc?db=hgEpdNew&format=genome&entry=$$ color 50,50,200 priority 1 track epdNewPromoterNonCoding shortLabel EPDnew NC v1 longLabel ncRNA promoters from EPDnewNC human version 001 parent epdNew on bigDataUrl /gbdb/$D/bbi/epdNewHumanNc001.$D.bb dataVersion EPDNewNC Human Version 001 (April 2019) url https://epd.epfl.ch/cgi-bin/get_doc?db=hsNCEpdNew&format=genome&entry=$$ color 180,0,134 priority 2 #RefSeq Select is a subtrack part of the RefSeq Composite in ../../refSeqComposite.ra #For more information on this change, see RM#24787 track ncbiRefSeqSelect parent refSeqComposite off priority 8 type genePred shortLabel RefSeq Select and MANE -longLabel NCBI RefSeq Select and MANE subset: one representative transcript per protein-coding gene +longLabel NCBI RefSeq Select and MANE subset: A single representative transcript trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons track clinGenCnv override filter.size 773:11309456 filterLimits.size 773:11309456 track covidHct shortLabel Transcription response longLabel High-confidence SARS-CoV-2 infection transcriptional response target genes priority 100 type bigBed 8 + color 150,20,20 mouseOver $_mouseOver : $name - CQV: $cqv - Rank: $rank group covid bigDataUrl /gbdb/hg38/covidHct/covidHct.bb release alpha include dbSnpOldHg38.ra beta,public include dbSnpArchiveHg38.ra alpha