e00c4ac98aed323e5dba0241250e4ee16369b573 jnavarr5 Mon Jun 3 13:58:55 2024 -0700 Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537 diff --git src/hg/makeDb/trackDb/mouse/trackDb.ra src/hg/makeDb/trackDb/mouse/trackDb.ra index 5e47267..7bebce3 100644 --- src/hg/makeDb/trackDb/mouse/trackDb.ra +++ src/hg/makeDb/trackDb/mouse/trackDb.ra @@ -1,881 +1,879 @@ # chainNet tracks include trackDb.chainNet.ra track knownGene shortLabel UCSC Genes longLabel UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics) group genes visibility pack color 12,12,120 type genePred knownGenePep knownGeneMrna exonNumbers on idXref kgAlias kgID alias hgGene on hgsid on directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s baseColorUseCds given baseColorDefault genomicCodons defaultLinkedTables kgXref intronGap 12 track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Chromosome Bands Based on Microscopy (for Ideogram) group map visibility dense altColor 150,50,50 type bed 4 + track cytoBand shortLabel Chromosome Band longLabel Chromosome Bands Based On Microscopy group map visibility hide altColor 150,50,50 type bed 4 + track recombRateMouse shortLabel Recomb Rate longLabel Recombination Rate from WI and MGD genetic maps (WI default) group map visibility hide type bed 4 + track gap override visibility hide track jaxQtl shortLabel MGI QTL longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics group map visibility hide color 200,100,0 type bed 6 + noScoreFilter . url http://www.informatics.jax.org/marker/$$ urlLabel MGI QTL Detail: track jaxQTL2 shortLabel MGI QTL longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics group map visibility hide color 200,100,0 type bed 8 + url http://www.informatics.jax.org/marker/$$ urlLabel MGI QTL Detail: track jaxQTL3 shortLabel MGI QTL longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics group map visibility hide color 200,100,0 type bed 8 + noScoreFilter . url http://www.informatics.jax.org/marker/$$ urlLabel MGI QTL Detail: track igtc shortLabel Gene Trap longLabel International Gene Trap Consortium Sequence Tag Alignments group genes visibility hide type psl . url http://www.genetrap.org/cgi-bin/annotation.py?cellline=$$ urlLabel IGTC Cell Line Annotation: track komp shortLabel IKMC Genes longLabel International Knockout Mouse Consortium Genes group genes visibility hide type bed 12 noScoreFilter . itemRgb on urlLabel KOMP Data Coordination Center: url http://www.mousephenotype.org/data/genes/$$ mgiUrlLabel MGI Report: mgiUrl http://www.informatics.jax.org/marker/$$ track ikmc shortLabel IKMC Genes longLabel International Knockout Mouse Consortium Genes group genes visibility hide type bed 12 noScoreFilter . itemRgb on urlLabel KOMP Data Coordination Center: url http://www.mousephenotype.org/data/genes/$$ mgiUrlLabel MGI Report: mgiUrl http://www.informatics.jax.org/marker/$$ track acembly shortLabel AceView Genes longLabel AceView Gene Models With Alt-Splicing group genes visibility hide color 155,0,125 type genePred acemblyPep acemblyMrna exonNumbers on autoTranslate 0 url https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&l=$$ itemClassTbl acemblyClass geneClasses main putative gClass_main 128,0,125 gClass_putative 200,0,125 urlLabel AceView Gene Summary: track slamHuman shortLabel Slam Human longLabel SLAM Gene Predictions Using Human/Mouse Homology group genes visibility hide color 100,50,0 altColor 175,150,128 type genePred track altGraphX shortLabel Alt-Splicing longLabel Alternative Splicing from ESTs/mRNAs group rna visibility hide type altGraphX track rikenCageTc shortLabel Riken CAGE TC longLabel Riken CAGE - Associated Transcript Clusters group rna visibility hide type bed 6 . origAssembly mm5 url http://fantom31p.gsc.riken.jp/cage_analysis/mm5/TSSSummary.php?tss_id=$$ track rikenCageCtss compositeTrack on shortLabel Riken CAGE longLabel Riken CAGE - Predicted Gene Start Sites group rna visibility hide type bedGraph 4 maxHeightPixels 128:16:16 minLimit 1 maxLimit 4316 viewLimits 1.0:10.0 windowingFunction mean autoScale Off origAssembly mm5 track rikenCageCtssPlus parent rikenCageCtss shortLabel Riken CAGE + longLabel Riken CAGE Plus Strand - Predicted Gene Start Sites priority 1 color 109,51,43 track rikenCageCtssMinus parent rikenCageCtss shortLabel Riken CAGE - longLabel Riken CAGE Minus Strand - Predicted Gene Start Sites priority 2 color 43,51,109 track jaxRepTranscript shortLabel MGI RepTranscrpt longLabel Jackson Laboratory / Mouse Genome Informatics Representative Transcript group phenoAllele visibility hide color 0,0,150 type genePred url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerDetail&id=$$ urlLabel MGI Gene Detail: baseColorUseCds none track jaxPhenotype shortLabel MGI Phenotype longLabel Jackson Laboratory / Mouse Genome Informatics Phenotype group phenoAllele visibility hide color 190,110,0 type bed 12 + noScoreFilter . url http://www.informatics.jax.org/searches/allele_report.cgi?markerID=$$ urlLabel MGI Phenotypic Allele(s): track jaxAllele shortLabel MGI Allele longLabel Jackson Laboratory / Mouse Genome Informatics Allele group phenoAllele visibility hide color 200, 0, 110 altColor 200, 0, 110 type bed 12 + noScoreFilter . url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$ urlLabel MGI Phenotypic Allele: html jaxAlleleOld track jaxGeneTrap shortLabel MGI Gene Trap longLabel Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps group phenoAllele visibility hide type bed 12 + itemRgb on noScoreFilter . url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$ urlLabel MGI Phenotypic Allele: track genotypeArrays compositeTrack on shortLabel Agilent CGH longLabel Agilent CGH Microarray probesets group varRep visibility hide noInherit on type bed 3 track agilentCgh1x1m parent genotypeArrays shortLabel Ag CGH 1x1M longLabel Agilent SurePrint G3 Mouse CGH Microarray 1x1M AMADID 027414 color 0,128,0 nextItemButton off noScoreFilter . type bed 4 . priority 1 track agilentCgh4x180k parent genotypeArrays shortLabel Ag CGH 4x180K longLabel Agilent SurePrint G3 Mouse CGH Microarray 4x180K AMADID 027411 color 255,128,0 nextItemButton off noScoreFilter . type bed 4 . priority 2 track agilentCgh244a parent genotypeArrays shortLabel Ag CGH 1x244K longLabel Agilent SurePrint HD Mouse CGH Microarray 1x244K AMADID 014695 color 0,128,0 exonArrows on nextItemButton off noScoreFilter . type bed 6 . priority 3 track agilentCgh105a parent genotypeArrays shortLabel Ag CGH 2x105K longLabel Agilent SurePrint HD Mouse CGH Microarray 2x105K AMADID 014699 color 255,128,0 exonArrows on nextItemButton off noScoreFilter . type bed 6 . priority 4 track gnfAtlas2 shortLabel GNF Atlas 2 longLabel GNF Expression Atlas 2 group regulation visibility hide type expRatio expScale 4.0 expStep 0.5 expTable gnfMouseAtlas2MedianExps # (expTable is kind of obselete) groupings gnfMouseAtlas2Groups track rinnSex shortLabel Rinn Sex Exp longLabel Rinn et al. Sex Gene Expression Data on MOE430A Chip group regulation visibility hide type expRatio expScale 8.0 expStep 1.0 expTable mouseRinnSexMedianExps # (expTable is kind of obselete) groupings rinnSexGroups track affyGnfU74A shortLabel GNF U74A longLabel GNF Expression Atlas on Mouse Affymetrix U74A Chip group regulation visibility hide type expRatio expScale 4.0 expStep 0.5 expTable gnfMouseU74aAllExps # (expTable is kind of obselete) groupings gnfMouseU74aGroups track affyGnfU74B shortLabel GNF U74B longLabel GNF Expression Atlas on Mouse Affymetrix U74B Chip group regulation visibility hide type expRatio expScale 4.0 expStep 0.5 expTable gnfMouseU74bAllExps # (expTable is kind of obselete) groupings gnfMouseU74bGroups track affyGnfU74C shortLabel GNF U74C longLabel GNF Expression Atlas on Mouse Affymetrix U74C Chip group regulation visibility hide type expRatio expScale 4.0 expStep 0.5 expTable gnfMouseU74cAllExps # (expTable is kind of obselete) groupings gnfMouseU74cGroups track affyGnf1m shortLabel Affy GNF1M longLabel Alignments of Probes from Affymetrix GNF1M Chip group regulation visibility hide type psl . track affyU74 shortLabel Affy U74 longLabel Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C) group regulation visibility hide type psl . track phastConsElements30way shortLabel Most Conserved longLabel PhastCons Conserved Elements group compGeno visibility hide exonArrows off showTopScorers 200 type bed 5 . track phastConsElements17way shortLabel Most Conserved longLabel PhastCons Conserved Elements group compGeno visibility hide exonArrows off showTopScorers 200 type bed 5 . track blatFugu override visibility dense track blastzBestMouse shortLabel Self Best longLabel $Organism Blastz Best-in-Genome Self Alignments group varRep visibility hide color 100,50,0 altColor 255,240,200 spectrum on type psl xeno mm3 otherDb mm3 track stsMapMouseNew shortLabel STS Markers longLabel STS Markers on Genetic and Radiation Hybrid Maps group map visibility dense altColor 128,128,255, type bed 5 + track affyMOE430 shortLabel Affy MOE430 longLabel Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B) group regulation visibility hide type psl . track regPotential7X shortLabel Reg Potential 7 species longLabel ESPERR Regulatory Potential (7 species) group regulation visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF color 0,128,255 altColor 255,128,0 viewLimits 0.0:0.10 windowingFunction mean spanList 1 type wig -1.0 1.0 track chainDanRer4NoRand shortLabel $o_db Chain NoRand longLabel $o_Organism ($o_date) Chained Alignments No Randoms group compGeno priority 159.04 visibility hide color 100,50,0 altColor 255,240,200 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 matrixHeader A, C, G, T spectrum on type chain danRer4 otherDb danRer4 track netDanRer4NoRand shortLabel $o_db Net NoRand longLabel $o_Organism ($o_date) Alignment Net No Randoms group compGeno priority 159.05 visibility hide spectrum on type netAlign danRer4 chainDanRer4NoRand otherDb danRer4 track blastzHg17 shortLabel Human Blastz longLabel $o_Organism ($o_date) Blastz Alignments group compGeno visibility hide color 100,50,0 altColor 255,240,200 spectrum on type psl xeno hg17 otherDb hg17 track syntenyNetHg17 shortLabel $o_Organism Syntenic Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno visibility hide spectrum on type netAlign hg17 chainHg17 otherDb hg17 track chainHg16 override shortLabel Hg16 Chain priority 279.7 track netHg16 shortLabel Hg16 Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 279.8 visibility hide spectrum on type netAlign hg16 chainHg16 otherDb hg16 track syntenyNetRn3 shortLabel $o_Organism Syntenic Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 280.5 visibility hide spectrum on type netAlign rn3 chainRn3 otherDb rn3 track patSeq override url https://www.lens.org/lens/bio/patseqanalyzer#psa/mus_musculus/latest/chromosome/$s/${-$}?appInClaims=1 searchTable cytoBand searchMethod exact searchType cytoBand shortCircuit 1 termRegex (x|y|[1-9][0-9]?)?(q[A-H][0-9]*)(\.[0-9]+)? searchPriority 8 padding 500000 searchTable gold searchMethod exact searchType gold shortCircuit 1 termRegex (AC|AF|AL|AY|BX|CAAA|CR)[0-9]+(\.[0-9]+)? searchPriority 8 searchName stsMapAliasMrnaAcc searchTable stsMapMouseNew searchType bed semiShortCircuit 1 shortCircuit 1 xrefTable stsAlias xrefQuery select trueName,alias from %s where alias like '%s' searchBoth on termRegex [a-z][a-z0-9][0-9]+ dontCheck [^[:space:]]+ searchDescription Alias of STS Marker searchPriority 11 padding 100000 searchName stsMapAliasComprehensive searchTable stsMapMouseNew searchType bed xrefTable stsAlias xrefQuery select trueName,alias from %s where alias like '%s' searchBoth on termRegex [^[:space:]]+ searchDescription Alias of STS Marker searchPriority 11 padding 100000 searchTable affyU74 searchMethod exact searchType psl shortCircuit 1 termRegex MG-U74:.+ searchPriority 16 termPrefix MG-U74: searchName affyU74NoChip searchTable affyU74 searchMethod exact searchType psl shortCircuit 1 termRegex [0-9]+[[:alnum:]_]*_at searchPriority 16 searchTable affyGnfU74A searchMethod exact searchType bed shortCircuit 1 termRegex MG-U74A:.+ searchPriority 16 termPrefix MG-U74A: searchTable affyGnfU74B searchMethod exact searchType bed shortCircuit 1 termRegex MG-U74B:.+ searchPriority 16 termPrefix MG-U74B: searchTable affyGnfU74C searchMethod exact searchType bed shortCircuit 1 termRegex MG-U74C:.+ searchPriority 16 termPrefix MG-U74C: searchName affyMOE430 searchTable affyMOE430 searchMethod exact searchType psl shortCircuit 1 termRegex (A:|B:)[0-9]+[[:alnum:]_]*_at searchPriority 16 searchName affyMOE430ChipPrefix searchTable affyMOE430 searchMethod exact searchType psl shortCircuit 1 termRegex MOE430(A|B):.+ searchPriority 16 termPrefix MOE430 searchName affyMOE430NoChip searchTable affyMOE430 searchMethod fuzzy searchType psl shortCircuit 1 termRegex [0-9]+[[:alnum:]_]*_at dontCheck (A:|B:)[0-9]+[[:alnum:]_]*_at searchPriority 16 searchTable affyGnf1m searchMethod exact searchType psl shortCircuit 1 termRegex gnf1m[0-9]+.+ searchPriority 16 searchName agilentCgh1x1m searchTable agilentCgh1x1m searchMethod prefix searchType bed shortCircuit 1 termRegex A_(53|67)_P[0-9]+ searchPriority 17.1 searchName agilentCgh244a searchTable agilentCgh244a searchMethod prefix searchType bed shortCircuit 1 termRegex A_(53|67)_P[0-9]+ searchPriority 17.2 searchName agilentCgh4x180k searchTable agilentCgh4x180k searchMethod prefix searchType bed shortCircuit 1 termRegex A_(53|67)_P[0-9]+ searchPriority 17.3 searchName agilentCgh105a searchTable agilentCgh105a searchMethod prefix searchType bed shortCircuit 1 termRegex A_(53|67)_P[0-9]+ searchPriority 17.4 searchName miRNAPrefix searchTable miRNA searchMethod prefix searchType bed shortCircuit 1 termRegex mmu-(mir|let)-[0-9]+[a-z]? dontCheck mmu-(mir|let)-[0-9]+[a-z]?(-[0-9]+)? searchPriority 18 searchTable miRNA searchMethod exact searchType bed shortCircuit 1 termRegex mmu-(mir|let)-.+ searchPriority 18.5 searchTable rikenCageTc searchMethod exact searchType bed shortCircuit 1 searchPriority 20 termPrefix rikenTC: searchTable jaxQtl searchType bed searchMethod fuzzy termRegex [a-z0-9-]+(.[123])? searchPriority 50 searchTable jaxQTL3 searchType bed searchMethod fuzzy termRegex [[:alpha:]0-9]+ searchPriority 50 searchTable jaxRepTranscript searchType genePred searchMethod fuzzy termRegex [^[:space:]]+ searchPriority 50 searchTable jaxPhenotype searchType bed searchMethod fuzzy termRegex [^[:space:]]+ searchPriority 50 searchTable jaxAllele searchType bed searchMethod fuzzy termRegex [^[:space:]]+ searchPriority 50 track bacEndPairs #replaces record bacEndPairs in parent dir missing/extra color,altColor shortLabel BAC End Pairs longLabel BAC End Pairs group map visibility hide type bed 6 + exonArrows off searchTable igtc searchType psl searchMethod prefix searchPriority 50 termRegex [A-Z0-9\._+-]+ track luNega shortLabel UCSC Pseudo longLabel UCSC Pseudogenes group genes type bed 12 visibility hide searchTable ctgPos searchMethod prefix shortCircuit 1 termRegex (NT_|NC_)[0-9]+([0-9\.]+)? query select chrom,chromStart,chromEnd,contig from %s where contig like '%s%%' searchPriority 5 searchTable komp searchType bed searchMethod exact searchPriority 5 termRegex [a-z0-9.-]+(_[a-z0-9]+)? searchName kompPrefix searchTable komp searchType bed searchMethod prefix searchPriority 5 termRegex [a-z0-9.-]+ dontCheck [a-z0-9.-]+_[a-z0-9]+ searchTable ikmc searchType bed searchMethod exact searchPriority 5 termRegex [a-z0-9.-]+(_[a-z0-9]+)? searchName ikmcPrefix searchTable ikmc searchType bed searchMethod prefix searchPriority 5 termRegex [a-z0-9.-]+ dontCheck [a-z0-9.-]+_[a-z0-9]+ track affyMOE430v2 shortLabel Affy MOE430v2 longLabel Alignments of Affymetrix Consensus Sequences from Mouse MOE430 version 2 group regulation visibility hide url https://www.affymetrix.com/LinkServlet?probeset=$$ type psl . track gnfMouseAtlas3 shortLabel GNF Atlas 3 longLabel GNF Expression Atlas 3 group regulation visibility hide type expRatio expScale 4.0 expStep 0.5 url http://biogps.gnf.org/?query=$$ urlLabel BioGPS: groupings gnfMouseAtlas3Groups track chainOtoGar1Best override priority 274.0 track ensGene override visibility dense track uniprot override hideEmptySubtracks off #facebase microarray track track FaceBase24SampleTypesAvg shortLabel FaceBase 24STypes longLabel FaceBase 24 Sample Types Averaged #priority 79.1 visibility hide type expRatio expScale 1.50 expStep 0.1 groupings facebase31_AllGroups group regulation #searchTable FaceBase_24Samp_Types_Averaged #searchType bed include cloneEnd.trackDb.ra track snp142Common shortLabel Common SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?do_not_redirect&rs=$$ urlLabel dbSNP: snpSeq snp142Seq snpExceptionDesc snp142ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp142CodingDbSnp, priority 1 html snp142Common track snp142Mult shortLabel Mult. SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?do_not_redirect&rs=$$ urlLabel dbSNP: snpSeq snp142Seq snpExceptionDesc snp142ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp142CodingDbSnp, html snp142Mult track snp142 shortLabel All SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?do_not_redirect&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp142CodingDbSnp, html snp142 searchTable snp142Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9861 padding 250 searchTable snp142Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9862 padding 250 searchTable snp142Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9863 padding 250 searchTable snp142 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9864 padding 250 -include jaspar.ra - include ../refSeqComposite.ra track ncbiRefSeqSelect parent refSeqComposite off priority 8 type genePred shortLabel RefSeq Select longLabel NCBI RefSeq Select: One representative transcript per protein-coding gene trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons