06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/makeDb/trackDb/rat/trackDb.ra src/hg/makeDb/trackDb/rat/trackDb.ra index 047e2b9..0e89a3e 100644 --- src/hg/makeDb/trackDb/rat/trackDb.ra +++ src/hg/makeDb/trackDb/rat/trackDb.ra @@ -1,322 +1,338 @@ # "$Id: trackDb.ra,v 1.82 2010/05/07 05:35:53 kent Exp $"; 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 +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 ISCN Lengths (for Ideogram) group map priority .1 visibility dense altColor 150,50,50 type bed 4 + track cytoBand shortLabel Chromosome Band longLabel Chromosome Bands Based On ISCN Lengths group map visibility hide altColor 150,50,50 type bed 4 + track recombRateRat shortLabel Recomb Rate longLabel Recombination Rate from SHRSPxBN and FHHxACI genetic maps (SHRSPxBN default) group map visibility hide type bed 4 + track bactigPos shortLabel Bactigs longLabel Bactigs group map visibility hide color 150,0,0 type bed 4 + track slamHuman shortLabel Slam Human longLabel Slam Gene Predictions Using Human/Rat Homology group genes priority 45.5 visibility hide color 100,50,0 altColor 175,150,128 type genePred track softberryGene override visibility dense track slamNonCodingHuman shortLabel Slam Non-Coding Human longLabel Slam Predictions of Human/Rat Conserved Non-Coding Regions group compGeno priority 120 visibility hide color 30,130,210 altColor 200,220,255 spectrum on type bed 5 . track twinscan override longLabel Twinscan Gene Predictions Using Rat/Human Homology visibility dense altColor 0,50,50 track sgpGene override longLabel SGP Gene Predictions Using Rat/Human Homology visibility dense track stsMapRat shortLabel STS Markers longLabel STS Markers on Genetic and Radiation Hybrid Maps group map priority 5 visibility dense altColor 128,128,255 type bed 5 + track blatFugu override priority 113 visibility dense track blatCi1 override priority 111 track genotypeArrays shortLabel Agilent CGH longLabel Agilent CGH Microarray probesets compositeTrack on group varRep visibility hide noInherit on type bed 3 track agilentCgh1x1m parent genotypeArrays shortLabel Ag CGH 1x1M longLabel Agilent SurePrint G3 Rat CGH Microarray 1x1M AMADID 027065 color 0,128,0 exonArrows on nextItemButton off noScoreFilter . type bed 4 . priority 1 track agilentCgh4x180k parent genotypeArrays shortLabel Ag CGH 4x180K longLabel Agilent SurePrint G3 Rat CGH Microarray 4x180K AMADID 027064 color 255,128,0 exonArrows on nextItemButton off noScoreFilter . type bed 4 . priority 2 track agilentCgh244a parent genotypeArrays shortLabel Ag CGH 1x244K longLabel Agilent SurePrint HD Rat CGH Microarray 1x244K AMADID 015223 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 Rat CGH Microarray 2x105K AMADID 015235 color 255,128,0 exonArrows on nextItemButton off noScoreFilter . type bed 6 . priority 4 track affyRAE230 shortLabel Affy RAE230 longLabel Alignments of Affymetrix Consensus Sequences from RAE230 group regulation visibility hide type psl . track affyU34A shortLabel Affy RG-U34A longLabel Alignments of Affymetrix Exemplar Sequences from RG-U34A group regulation visibility hide type psl . track gnfAtlas2 shortLabel GNF Atlas 2 longLabel GNF Rat U34A Expression Atlas 2 group regulation visibility hide type expRatio expScale 4.0 expStep 0.5 expTable gnfRatAtlas2MedianExps groupings gnfRatAtlas2Groups searchTable gold searchMethod exact searchType gold shortCircuit 1 termRegex RNOR[0-9]{8} searchPriority 8 searchName stsMapAliasMrnaAcc searchTable stsMapRat 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]+ searchDescription Alias of STS Marker searchPriority 11 padding 100000 searchName stsMapAliasComprehensive searchTable stsMapRat 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 bactigPos searchMethod exact searchType bed shortCircuit 1 termRegex [gkt][a-z]{3}(_[gkt][a-z]{3})?(_[0-9]+)? searchPriority 15 searchName miRNAPrefix searchTable miRNA searchMethod prefix searchType bed shortCircuit 1 termRegex rno-(mir|let)-[0-9]+[a-z]? dontCheck rno-(mir|let)-[0-9]+[a-z]?(-[0-9]+)? searchPriority 18 searchTable miRNA searchMethod exact searchType bed shortCircuit 1 termRegex rno-(mir|let)-.+ searchPriority 18.5 searchTable affyRAE230 searchMethod exact searchType psl shortCircuit 1 termRegex RAE230[A|B]:.+ dontCheck [A|B]:.+ searchPriority 15 termPrefix RAE230 searchName affyRAE230NoChip searchTable affyRAE230 searchMethod exact searchType psl shortCircuit 1 termRegex [A|B]:.+ searchPriority 15 searchTable affyU34A searchMethod exact searchType psl shortCircuit 1 termRegex RG-U34A:.+ dontCheck [A-Z0-9]+[[:alnum:]_]+.*_at searchPriority 16 termPrefix RG-U34A: searchName affyU34ANoChip searchTable affyU34A searchMethod exact searchType psl shortCircuit 1 termRegex A:.+ dontCheck [A-Z0-9]+[[:alnum:]_]+.*_at searchPriority 15 termPrefix A: searchName affyU34AAbbrev searchTable affyU34A searchMethod exact searchType psl shortCircuit 1 termRegex [A-Z0-9]+[[:alnum:]_]+.*_at searchPriority 15 searchName agilentCgh1x1m searchTable agilentCgh1x1m searchMethod prefix searchType bed shortCircuit 1 termRegex A_86_P[0-9]+ searchPriority 17.1 searchName agilentCgh244a searchTable agilentCgh244a searchMethod prefix searchType bed shortCircuit 1 termRegex A_86_P[0-9]+ searchPriority 17.2 searchName agilentCgh4x180k searchTable agilentCgh4x180k searchMethod prefix searchType bed shortCircuit 1 termRegex A_86_P[0-9]+ searchPriority 17.3 searchName agilentCgh105a searchTable agilentCgh105a searchMethod prefix searchType bed shortCircuit 1 termRegex A_86_P[0-9]+ searchPriority 17.4 track genieKnown override visibility pack track refGene override release public visibility pack track nscanGene override visibility dense track mrna override visibility dense track intronEst override visibility dense track est override visibility hide track rnaCluster override visibility hide track cpgIsland override visibility hide track rmsk override visibility dense