96b2dc6c40d4b9b6790fc71a5e217e275695e01f hiram Wed Jun 18 13:58:59 2025 -0700 initial trackDb from the GenArk hub refs #35898 diff --git src/hg/makeDb/trackDb/rat/rn8/genArk.trackDb.ra src/hg/makeDb/trackDb/rat/rn8/genArk.trackDb.ra new file mode 100644 index 00000000000..9f5234d5349 --- /dev/null +++ src/hg/makeDb/trackDb/rat/rn8/genArk.trackDb.ra @@ -0,0 +1,594 @@ +track assembly +longLabel Assembly +shortLabel Assembly +visibility hide +colorByStrand 150,100,30 230,170,40 +color 150,100,30 +altColor 230,170,40 +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.assembly.bb +type bigBed 6 +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.assembly +searchIndex name +searchTrix /gbdb/genark/GCF/036/323/735/GCF_036323735.1/ixIxx/GCF_036323735.1_GRCr8.assembly.ix +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Nucleotide database: +group map + +track cytoBandIdeo +shortLabel Chromosome Band (Ideogram) +longLabel Ideogram for Orientation +group map +visibility dense +type bigBed 4 + +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.cytoBand.bb + +track gc5Base +shortLabel GC Percent +longLabel GC Percent in 5-Base Windows +group map +visibility dense +autoScale Off +maxHeightPixels 128:36:16 +graphTypeDefault Bar +gridDefault OFF +windowingFunction Mean +color 0,0,0 +altColor 128,128,128 +viewLimits 30:70 +type bigWig 0 100 +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.gc5Base.bw +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.gc5Base + +track tanDups +shortLabel Tandem Dups +longLabel Paired identical sequences +compositeTrack on +visibility hide +type bigBed 12 +group map +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.tanDups + +track gapOverlap +parent tanDups on +shortLabel Gap Overlaps +longLabel Paired exactly identical sequence on each side of a gap +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.gapOverlap.bb +type bigBed 12 + +track tandemDups +parent tanDups on +shortLabel Tandem Dups +longLabel Paired exactly identical sequence survey over entire genome assembly +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.tandemDups.bb +type bigBed 12 + +track repeatMasker +shortLabel RepeatMasker +longLabel RepeatMasker Repetitive Elements +type bigRmsk 9 + +visibility pack +group varRep +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.rmsk.bb +maxWindowToDraw 5000000 +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.repeatMasker + +track repeatModeler +shortLabel RepeatModeler +longLabel RepeatModeler Repetitive Elements +type bigRmsk 9 + +visibility hide +group varRep +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.rModel.bb +xrefDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.rModel.align.bb +maxWindowToDraw 5000000 +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.repeatModeler + +track simpleRepeat +shortLabel Simple Repeats +longLabel Simple Tandem Repeats by TRF +group varRep +visibility dense +type bigBed 4 + +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.simpleRepeat.bb +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.simpleRepeat + +track refSeqComposite +compositeTrack on +shortLabel NCBI RefSeq +longLabel RefSeq gene predictions from NCBI +group genes +visibility pack +type bigBed +dragAndDrop subTracks +allButtonPair on +dataVersion NCBI RefSeq GCF_036323735.1-RS_2024_02 (2024-02-24) +html /gbdb/genark/GCF/036/323/735/GCF_036323735.1/html/GCF_036323735.1_GRCr8.refSeqComposite +priority 2 + +track ncbiRefSeq +parent refSeqComposite on +color 12,12,120 +shortLabel RefSeq All +type bigGenePred +urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" +labelFields name,geneName,geneName2 +defaultLabelFields geneName2 +searchIndex name +searchTrix /gbdb/genark/GCF/036/323/735/GCF_036323735.1/ixIxx/GCF_036323735.1_GRCr8.ncbiRefSeq.ix +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.ncbiRefSeq.bb +longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) +idXref ncbiRefSeqLink mrnaAcc name +baseColorUseCds given +baseColorDefault genomicCodons +priority 1 + +track ncbiRefSeqCurated +color 12,12,120 +parent refSeqComposite on +shortLabel RefSeq Curated +longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) +type bigGenePred +urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" 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/gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.ncbiRefSeqPredicted.bb +baseColorUseCds given +baseColorDefault genomicCodons +priority 3 + +track ncbiRefSeqOther +color 32,32,32 +parent refSeqComposite on +shortLabel RefSeq Other +longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) +priority 4 +searchIndex name +searchTrix /gbdb/genark/GCF/036/323/735/GCF_036323735.1/ixIxx/GCF_036323735.1_GRCr8.ncbiRefSeqOther.ix +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.ncbiRefSeqOther.bb +type bigBed 12 + +labelFields name +skipEmptyFields on +urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" + +track ncbiRefSeqPsl +priority 5 +parent refSeqComposite off +shortLabel RefSeq Alignments +longLabel RefSeq Alignments of RNAs +type bigPsl +searchIndex name +bigDataUrl /gbdb/genark/GCF/036/323/735/GCF_036323735.1/bbi/GCF_036323735.1_GRCr8.bigPsl.bb +indelDoubleInsert on +indelQueryInsert on +showDiffBasesAllScales . +showDiffBasesMaxZoom 10000.0 +showCdsMaxZoom 10000.0 +showCdsAllScales . +baseColorDefault diffCodons +pslSequence no +baseColorUseSequence lfExtra +baseColorUseCds table given +color 0,0,0 + +track ncbiRefSeqSelect +parent refSeqComposite off +priority 7 +type bigGenePred +shortLabel RefSeq Select +longLabel NCBI RefSeq/MANE Select: one representative transcript per protein-coding gene +idXref ncbiRefSeqLink mrnaAcc name +color 20,20,160 +labelFields name,geneName,geneName2 +searchIndex name +searchTrix 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