083d201617a2e46b63f16cb8ee7d977fb5a7f0be hiram Wed Jun 18 15:00:42 2025 -0700 initial trackDb from GenArk refs #35898 diff --git src/hg/makeDb/trackDb/chicken/galGal7w/genArk.trackDb.ra src/hg/makeDb/trackDb/chicken/galGal7w/genArk.trackDb.ra new file mode 100644 index 00000000000..405459ef814 --- /dev/null +++ src/hg/makeDb/trackDb/chicken/galGal7w/genArk.trackDb.ra @@ -0,0 +1,389 @@ +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/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.assembly.bb +type bigBed 6 +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.assembly +searchIndex name +searchTrix /gbdb/genark/GCF/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.assembly.ix +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Nucleotide database: +group map + +track gap +longLabel AGP gap +shortLabel Gap (AGP defined) +visibility hide +color 0,0,0 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.gap.bb +type bigBed 4 +group map +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.gap + +track cytoBandIdeo +shortLabel Chromosome Band (Ideogram) +longLabel Ideogram for Orientation +group map +visibility dense +type bigBed 4 + +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.gc5Base.bw +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.gc5Base + +track tanDups +shortLabel Tandem Dups +longLabel Paired identical sequences +compositeTrack on +visibility hide +type bigBed 12 +group map +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.tanDups + +track gapOverlap +parent tanDups on +shortLabel Gap Overlaps +longLabel Paired exactly identical sequence on each side of a gap +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.tandemDups.bb +type bigBed 12 + +track repeatMasker +shortLabel RepeatMasker +longLabel RepeatMasker Repetitive Elements +type bigRmsk 9 + +visibility pack +group varRep +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.rmsk.bb +xrefDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.rmsk.align.bb +maxWindowToDraw 5000000 +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.repeatMasker + +track repeatModeler +shortLabel RepeatModeler +longLabel RepeatModeler Repetitive Elements +type bigRmsk 9 + +visibility hide +group varRep +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.rModel.bb +xrefDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.rModel.align.bb +maxWindowToDraw 5000000 +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.repeatModeler + +track simpleRepeat +shortLabel Simple Repeats +longLabel Simple Tandem Repeats by TRF +group varRep +visibility dense +type bigBed 4 + +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.simpleRepeat.bb +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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 Gallus gallus Annotation Release 106 (2022-04-13) +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ncbiRefSeq.ix +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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/$$" +labelFields name,geneName,geneName2 +defaultLabelFields geneName2 +searchIndex name +searchTrix /gbdb/genark/GCF/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ncbiRefSeqCurated.ix +idXref ncbiRefSeqLink mrnaAcc name +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ncbiRefSeqCurated.bb +baseColorUseCds given +baseColorDefault genomicCodons +priority 2 + +track ncbiRefSeqPredicted +color 12,12,120 +parent refSeqComposite on +shortLabel RefSeq Predicted +longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) +type bigGenePred +urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" 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/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ncbiRefSeqPredicted.ix +idXref ncbiRefSeqLink mrnaAcc name +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ncbiRefSeqOther.ix +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.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 cpgIslands +compositeTrack on +shortLabel CpG Islands +longLabel CpG Islands (Islands < 300 Bases are Light Green) +group regulation +visibility dense +type bigBed 4 + +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.cpgIslands + +track cpgIslandExt +parent cpgIslands off +shortLabel CpG Islands +longLabel CpG Islands (Islands < 300 Bases are Light Green) +type bigBed 4 + +priority 1 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.cpgIslandExt.bb + +track cpgIslandExtUnmasked +parent cpgIslands on +shortLabel Unmasked CpG +longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) +type bigBed 4 + +priority 2 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.cpgIslandExtUnmasked.bb + +track windowMasker +shortLabel WM + SDust +longLabel Genomic Intervals Masked by WindowMasker + SDust +group varRep +visibility dense +type bigBed 3 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.windowMasker.bb +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.windowMasker + +track allGaps +shortLabel All Gaps +longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps +group map +visibility hide +type bigBed 3 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.allGaps.bb +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.allGaps + +track augustus +shortLabel Augustus +longLabel Augustus Gene Predictions +group genes +visibility dense +color 180,0,0 +type bigGenePred +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.augustus.bb +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.augustus + +track xenoRefGene +shortLabel RefSeq mRNAs +longLabel RefSeq mRNAs mapped to this assembly +group rna +visibility pack +color 180,0,0 +type bigGenePred +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.xenoRefGene.bb +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Nucleotide database: +labelFields name,geneName,geneName2 +defaultLabelFields geneName +searchIndex name +searchTrix /gbdb/genark/GCF/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.xenoRefGene.ix +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.xenoRefGene + +track ensGene +shortLabel Ensembl genes +longLabel Ensembl genes 2022_01 +group genes +priority 40 +visibility pack +color 150,0,0 +itemRgb on +type bigGenePred +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ensGene.bb +searchTrix /gbdb/genark/GCF/016/700/215/GCF_016700215.2/ixIxx/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ensGene.ix +searchIndex name +labelFields name,name2 +defaultLabelFields name2 +baseColorUseCds given +baseColorDefault genomicCodons +labelSeparator " " +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.ensGene +############################################################################## +# galGal6 - Chicken - Gallus gallus - taxId: 9031 +############################################################################## + +track chainNetGalGal6 +compositeTrack on +shortLabel Chicken Chain/Net +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +priority 100.1 +color 0,0,0 +altColor 100,50,0 +type bed 3 +sortOrder view=+ +matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +chainMinScore 5000 +chainLinearGap loose +matrixHeader A, C, G, T +otherDb galGal6 +html /gbdb/genark/GCF/016/700/215/GCF_016700215.2/html/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainNet + +track chainNetGalGal6Viewchain +shortLabel Chain +view chain +visibility pack +parent chainNetGalGal6 +spectrum on + +track chainGalGal6 +parent chainNetGalGal6Viewchain +subGroups view=chain +shortLabel Chicken Chain +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Chained Alignments +type bigChain galGal6 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainGalGal6.bb +linkDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainGalGal6Link.bb +priority 1 + +track chainSynGalGal6 +parent chainNetGalGal6Viewchain +subGroups view=chain +shortLabel Chicken synChain +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Syntenic Chained Alignments +type bigChain galGal6 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainSynGalGal6.bb +linkDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainSynGalGal6Link.bb +priority 2 + +track chainRBestGalGal6 +parent chainNetGalGal6Viewchain +subGroups view=chain +shortLabel Chicken rbChain +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Reciprocal Best Chained Alignments +type bigChain galGal6 +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainRBestGalGal6.bb +linkDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.chainRBestGalGal6Link.bb +priority 3 + +track mafNetGalGal6Viewnet +shortLabel Net +view net +visibility full +parent chainNetGalGal6 + +track netGalGal6 +parent mafNetGalGal6Viewnet +subGroups view=net +shortLabel Chicken net +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Net Alignment +type bigMaf +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.galGal6.net.bb +summary /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.galGal6.net.summary.bb +speciesOrder galGal6 +priority 4 + +track synNetGalGal6 +parent mafNetGalGal6Viewnet +subGroups view=net +shortLabel Chicken synNet +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Syntenic Net Alignment +type bigMaf +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.galGal6.synNet.bb +summary /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.galGal6.synNet.summary.bb +speciesOrder galGal6 +priority 5 + +track rbestNetGalGal6 +parent mafNetGalGal6Viewnet +subGroups view=net +shortLabel Chicken rbestNet +longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Reciprocal Best Net Alignment +type bigMaf +bigDataUrl /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.galGal6.rbestNet.bb +summary /gbdb/genark/GCF/016/700/215/GCF_016700215.2/bbi/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w.galGal6.rbestNet.summary.bb +speciesOrder galGal6 +priority 6