098e7866ab59c5c6b0c4c77919350d637894d113 markd Wed Apr 28 00:38:42 2021 -0700 transMap V6 diff --git src/hg/makeDb/trackDb/trackDb.transMap.ra src/hg/makeDb/trackDb/trackDb.transMap.ra index c79dc36..b8d62bb 100644 --- src/hg/makeDb/trackDb/trackDb.transMap.ra +++ src/hg/makeDb/trackDb/trackDb.transMap.ra @@ -1,253 +1,388 @@ +############################################################################# +# V4 +############################################################################# track transMap superTrack on shortLabel TransMap longLabel TransMap Alignments group genes track transMapV4 superTrack on shortLabel TransMap V4 longLabel TransMap Alignments Version 4 html transMap group genes track transMapEnsemblV4 superTrack transMapV4 pack shortLabel TransMap Ensembl longLabel TransMap Ensembl and GENCODE Mappings Version 4 html transMapEnsembl transMapSrcSet ensembl group genes type bigPsl priority 10.001 color 0,100,0 canPack on visibility pack baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId,geneType,transcriptType defaultLabelFields orgAbbrev,geneName labelSeparator " " bigDataUrl /gbdb/$D/transMap/V4/$D.ensembl.transMapV4.bigPsl searchIndex name,srcTransId,geneName,geneId searchTable transMapEnsemblV4 searchType bigPsl track transMapRefSeqV4 superTrack transMapV4 pack shortLabel TransMap RefGene longLabel TransMap RefSeq Gene Mappings Version 4 html transMapRefSeq transMapSrcSet refseq group genes type bigPsl priority 10.003 color 0,100,0 canPack on visibility pack baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId defaultLabelFields orgAbbrev,geneName labelSeparator " " bigDataUrl /gbdb/$D/transMap/V4/$D.refseq.transMapV4.bigPsl searchIndex name,srcTransId,geneName,geneId searchTable transMapRefSeqV4 searchType bigPsl track transMapRnaV4 superTrack transMapV4 pack shortLabel TransMap RNA longLabel TransMap GenBank RNA Mappings Version 4 html transMapRna transMapSrcSet rna group genes type bigPsl priority 10.004 color 0,100,0 canPack on visibility pack baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName defaultLabelFields orgAbbrev,srcTransId labelSeparator " " bigDataUrl /gbdb/$D/transMap/V4/$D.rna.transMapV4.bigPsl searchIndex name,srcTransId,geneName searchTable transMapRnaV4 searchType bigPsl track transMapEstV4 superTrack transMapV4 hide shortLabel TransMap ESTs longLabel TransMap EST Mappings Version 4 html transMapEst transMapSrcSet est group genes type bigPsl priority 10.005 color 0,100,0 canPack on visibility hide baseColorDefault none baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name defaultLabelFields orgAbbrev,srcTransId labelSeparator " " bigDataUrl /gbdb/$D/transMap/V4/$D.est.transMapV4.bigPsl searchIndex name,srcTransId searchTable transMapEstV4 searchType bigPsl +############################################################################# +# V5 +############################################################################# + track transMapV5 superTrack on shortLabel TransMap V5 longLabel TransMap Alignments Version 5 html transMapV5 group genes track transMapEnsemblV5 superTrack transMapV5 pack shortLabel TransMap Ensembl longLabel TransMap Ensembl and GENCODE Mappings Version 5 html transMapEnsembl transMapSrcSet ensembl group genes type bigPsl priority 10.001 color 0,100,0 canPack on visibility pack baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId,geneType,transcriptType defaultLabelFields orgAbbrev,geneName labelSeparator " " bigDataUrl /gbdb/$D/transMap/V5/$D.ensembl.transMapV5.bigPsl searchIndex name,srcTransId,geneName,geneId searchTable transMapEnsemblV5 searchType bigPsl track transMapRefSeqV5 superTrack transMapV5 pack shortLabel TransMap RefGene longLabel TransMap RefSeq Gene Mappings Version 5 html transMapRefSeq transMapSrcSet refseq group genes type bigPsl priority 10.003 color 0,100,0 canPack on visibility pack baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId defaultLabelFields orgAbbrev,geneName labelSeparator " " bigDataUrl /gbdb/$D/transMap/V5/$D.refseq.transMapV5.bigPsl searchIndex name,srcTransId,geneName,geneId searchTable transMapRefSeqV5 searchType bigPsl track transMapRnaV5 superTrack transMapV5 hide shortLabel TransMap RNA longLabel TransMap GenBank RNA Mappings Version 5 html transMapRna transMapSrcSet rna group genes type bigPsl priority 10.004 color 0,100,0 canPack on visibility hide baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName defaultLabelFields orgAbbrev,srcTransId labelSeparator " " bigDataUrl /gbdb/$D/transMap/V5/$D.rna.transMapV5.bigPsl searchIndex name,srcTransId,geneName searchTable transMapRnaV5 searchType bigPsl track transMapEstV5 superTrack transMapV5 hide shortLabel TransMap ESTs longLabel TransMap EST Mappings Version 5 html transMapEst transMapSrcSet est group genes type bigPsl priority 10.005 color 0,100,0 canPack on visibility hide baseColorDefault none baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 labelFields commonName,orgAbbrev,srcDb,srcTransId,name defaultLabelFields orgAbbrev,srcTransId labelSeparator " " bigDataUrl /gbdb/$D/transMap/V5/$D.est.transMapV5.bigPsl searchIndex name,srcTransId searchTable transMapEstV5 searchType bigPsl + +############################################################################# +# V6 +############################################################################# + +track transMapV6 +superTrack on +shortLabel TransMap V6 +longLabel TransMap Alignments Version 5 +html transMapV6 +group genes + + track transMapEnsemblV6 + superTrack transMapV6 pack + shortLabel TransMap Ensembl + longLabel TransMap Ensembl and GENCODE Mappings Version 5 + html transMapEnsembl + transMapSrcSet ensembl + group genes + type bigPsl + priority 10.001 + color 0,100,0 + canPack on + visibility pack + baseColorDefault diffCodons + baseColorUseCds given + baseColorUseSequence lfExtra + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + showCdsAllScales . + showCdsMaxZoom 10000.0 + labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId,geneType,transcriptType + defaultLabelFields orgAbbrev,geneName + labelSeparator " " + bigDataUrl /gbdb/$D/transMap/V6/$D.ensembl.transMapV6.bigPsl + searchIndex name,srcTransId,geneName,geneId + +searchTable transMapEnsemblV6 +searchType bigPsl + + track transMapRefSeqV6 + superTrack transMapV6 pack + shortLabel TransMap RefGene + longLabel TransMap RefSeq Gene Mappings Version 5 + html transMapRefSeq + transMapSrcSet refseq + group genes + type bigPsl + priority 10.003 + color 0,100,0 + canPack on + visibility pack + baseColorDefault diffCodons + baseColorUseCds given + baseColorUseSequence lfExtra + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + showCdsAllScales . + showCdsMaxZoom 10000.0 + labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId + defaultLabelFields orgAbbrev,geneName + labelSeparator " " + bigDataUrl /gbdb/$D/transMap/V6/$D.refseq.transMapV6.bigPsl + searchIndex name,srcTransId,geneName,geneId + +searchTable transMapRefSeqV6 +searchType bigPsl + + track transMapRnaV6 + superTrack transMapV6 hide + shortLabel TransMap RNA + longLabel TransMap GenBank RNA Mappings Version 5 + html transMapRna + transMapSrcSet rna + group genes + type bigPsl + priority 10.004 + color 0,100,0 + canPack on + visibility hide + baseColorDefault diffCodons + baseColorUseCds given + baseColorUseSequence lfExtra + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + showCdsAllScales . + showCdsMaxZoom 10000.0 + labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName + defaultLabelFields orgAbbrev,srcTransId + labelSeparator " " + bigDataUrl /gbdb/$D/transMap/V6/$D.rna.transMapV6.bigPsl + searchIndex name,srcTransId,geneName + +searchTable transMapRnaV6 +searchType bigPsl + + track transMapEstV6 + superTrack transMapV6 hide + shortLabel TransMap ESTs + longLabel TransMap EST Mappings Version 5 + html transMapEst + transMapSrcSet est + group genes + type bigPsl + priority 10.005 + color 0,100,0 + canPack on + visibility hide + baseColorDefault none + baseColorUseSequence lfExtra + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + labelFields commonName,orgAbbrev,srcDb,srcTransId,name + defaultLabelFields orgAbbrev,srcTransId + labelSeparator " " + bigDataUrl /gbdb/$D/transMap/V6/$D.est.transMapV6.bigPsl + searchIndex name,srcTransId + +searchTable transMapEstV6 +searchType bigPsl