## # map ## track gap shortLabel Gap longLabel Gap Locations group map visibility hide type bigBed 3 bigDataUrl gap.bigBed track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility hide 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 gc5Base.bigWig html gc5Base track hifi_20k track winnowmap_ont shortLabel Winnowmap ONT SVs longLabel Winnowmap ONT SVs superTrack on hide visibility hide group map priority 100 track winnowmap_ont_all parent winnowmap_ont shortLabel Winnowmap ONT Alignments longLabel Winnowmap ONT Alignments priority 1 type bam visibility hide bigDataUrl winnowmap_ont/winnowmap_ont_all.bam group map html winnowmap_ont_all track winnowmap_ont_ul parent winnowmap_ont shortLabel Winnowmap ONT Ultra-long Alignments longLabel Winnowmap ONT Ultra-long Alignments (at least 100kb) priority 2 type bam visibility hide bigDataUrl winnowmap_ont/winnowmap_ont_ul.bam group map html winnowmap_ont_ul track winnowmap_ont_all_variants parent winnowmap_ont shortLabel Winnowmap ONT Variants longLabel Winnowmap ONT Variants type vcfTabix maxWindowToDraw 200000 bigDataUrl winnowmap_ont/winnowmap_ont_all_variants.vcf.gz priority 3 visibility hide group map html winnowmap_ont_all_variants track winnowmap_pb shortLabel Winnowmap PacBio SVs longLabel Winnowmap PackBio SVs superTrack on hide visibility hide group map priority 101 track winnowmap_pb_clr parent winnowmap_pb shortLabel Winnowmap PacBio CLR Alignments longLabel Winnowmap PacBio CLR Alignments priority 1 type bam visibility hide bigDataUrl winnowmap_pb/winnowmap_pb_clr.bam group map html winnowmap_pb_clr.html track winnowmap_pb_hifi parent winnowmap_pb shortLabel Winnowmap PacBio HiFi Alignments longLabel Winnowmap PacBio HiFi Alignments priority 2 type bam visibility hide bigDataUrl winnowmap_pb/winnowmap_pb_hifi.bam group map html winnowmap_pb_hifi.html track illumina_pcrfree shortLabel Illumina PCRfree longLabel Illumina PCRfree superTrack on hide visibility hide group map priority 102 html illumina_pcrfree.html track illumina_pcrfree_aligns parent illumina_pcrfree shortLabel Illumina PCRfree Alignments longLabel Illumina PCRfree Alignments priority 1 type bam visibility hide bigDataUrl illumina_pcrfree/illumina_pcrfree.bam group map html illumina_pcrfree.html track illumina_pcrfree_variants parent illumina_pcrfree shortLabel Illumina PCRfree Variants longLabel Illumina PCRfree Variants type vcfTabix maxWindowToDraw 200000 bigDataUrl illumina_pcrfree/illumina_pcrfree_variants.vcf.gz priority 3 visibility hide group map html illumina_pcrfree_variants.html track bionano_cover shortLabel Bionano Coverage longLabel Bionano Coverage type bigWig 0.0 100.0 color 60,60,140 altColor 140,60,60 visibility hide bigDataUrl bionano_cover.bigWig group map priority 103 track kmer_metric shortLabel Kmer Metric longLabel Kmer Metric type bigWig 0.0 100.0 color 60,60,140 altColor 140,60,60 visibility hide bigDataUrl kmer_metric.bigWig group map priority 104 include fosmidABC10.txt ## # cenTelo ## track cenRegions shortLabel Centromere Regions longLabel Centromere Regions group cenTelo type bigBed visibility hide color 218,165,32 bigDataUrl cenRegions.bigBed priority 1 track telomereRegions shortLabel Telomere Regions longLabel Telomere Regions group cenTelo type bigBed visibility hide color 32,165,218 bigDataUrl telomereRegions.bigBed priority 1.1 track cenSat_annotation shortLabel CenSat Annotation longLabel Centromeric Satellite Annotation group cenTelo visibility hide itemRgb on maxItems 100000 type bigBed 9 + bigDataUrl cenSat_annotation.bigBed priority 2 track as_hor_annotation shortLabel AS HOR annotation longLabel Alpha satellite higher-order repeats annotation group cenTelo visibility hide type bigBed 9 itemRgb on maxItems 100000 bigDataUrl as_hor_annotation.bigBed priority 3 track as_sf_annotation shortLabel AS SF annotation longLabel Alpha satellite suprachromosomal Families and pericentromeric monomer layers annotation group cenTelo visibility hide type bigBed 9 itemRgb on maxItems 100000 bigDataUrl as_sf_annotation.bigBed priority 4 track as_strand shortLabel AS strand longLabel alpha satellite higher-order repeats strand orientation group cenTelo visibility hide type bigBed 9 itemRgb on maxItems 100000 bigDataUrl as_strand.bigBed priority 4.1 track hor_decompositions shortLabel HOR annotation longLabel Centromere HOR annotation group cenTelo visibility hide itemRgb on maxItems 100000 type bigBed 9 bigDataUrl hor_decompositions.bigBed priority 5 track hor_decompositions_native shortLabel HOR annotation native longLabel Centromere HOR annotation native group cenTelo visibility hide itemRgb on maxItems 100000 type bigBed 9 bigDataUrl hor_decompositions_native.bigBed priority 6 ## # varRep ## track rmsk shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep visibility hide itemRgb on maxItems 100000 type bigBed 9 + bigDataUrl rmsk.bigBed maxWindowToDraw 10000000 priority 1 track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility hide type bigBed 4 + bigDataUrl trf.bigBed priority 2 track sedefSegDups shortLabel SEDEF Segmental Dups longLabel Segmental Duplications group varRep visibility hide itemRgb on maxItems 100000 type bigBed 9 bigDataUrl sedefSegDups/sedefSegDups.bigBed priority 5 html sedefSegDups.html track sedefSegDupsLow shortLabel SEDEF Segmental Dups Low Id longLabel SEDEF Segmental Duplications Low Identity group varRep visibility hide itemRgb on maxItems 100000 type bigBed 9 bigDataUrl sedefSegDups/sedefSegDupsLow.bigBed html sedefSegDups.html priority 7 html sedefSegDups.html track hg002_hifiasm shortLabel HG002 hifiasm alignments longLabel HG002 hifiasm assembly alignments superTrack on hide visibility hide group varRep priority 100 html hg002Aligns.html track hg002_hifiasm_mat_nucmer parent hg002_hifiasm shortLabel HG002 maternal nucmer longLabel HG002 maternal haplotype nucmer alignments priority 1 type bam visibility hide bigDataUrl hg002Aligns/HG002-v0.11.mat.nucmer.t2tChm13_20200727.bam group varRep html hg002Aligns.html track hg002_hifiasm_pat_nucmer parent hg002_hifiasm shortLabel HG002 paternal nucmer longLabel HG002 paternal haplotype nucmer alignments priority 1 type bam visibility hide bigDataUrl hg002Aligns/HG002-v0.11.pat.nucmer.t2tChm13_20200727.bam group varRep html hg002Aligns.html track hg002_hifiasm_mat_minimap2 parent hg002_hifiasm shortLabel HG002 maternal minimap2 longLabel HG002 maternal haplotype minimap2 alignments priority 1 type bam visibility hide bigDataUrl hg002Aligns/HG002-v0.11.mat.minimap2.t2tChm13_20200727.bam group varRep html hg002Aligns.html track hg002_hifiasm_pat_minimap2 parent hg002_hifiasm shortLabel HG002 paternal minimap2 longLabel HG002 paternal haplotype minimap2 alignments priority 1 type bam visibility hide bigDataUrl hg002Aligns/HG002-v0.11.pat.minimap2.t2tChm13_20200727.bam group varRep html hg002Aligns.html include hgdp_wssd_cn.trackDb.txt include hgdp_wssd_cn_subset.trackDb.txt ## # comparative genomics ## track grch38Lastz compositeTrack off shortLabel GRCh38 LASTZ Alignment longLabel GRCh38 LASTZ Alignments visibility hide priority 30 type bigChain hg38 group compGeno html needTrackDescription.html track grch38AllChains parent grch38Lastz shortLabel GRCh38 All Chains longLabel GRCh38 LASTZ All Alignment Chains type bigChain hg38 color 20,0,120 visibility hide bigDataUrl grch38/t2tChm13_20200727.hg38.all.bigChain linkDataUrl grch38/t2tChm13_20200727.hg38.all.bigLink priority 1 group compGeno track grch38AllPrimaryChains parent grch38Lastz shortLabel GRCh38 All Primary Chains longLabel GRCh38 LASTZ All Alignment Chains from GRCh38 primary assembly type bigChain hg38 color 20,120,0 visibility hide bigDataUrl grch38/t2tChm13_20200727.hg38.all-primary.bigChain linkDataUrl grch38/t2tChm13_20200727.hg38.all-primary.bigLink priority 2 group compGeno track grch38OverChains parent grch38Lastz shortLabel GRCh38 Liftover Chains longLabel GRCh38 LASTZ Liftover Alignment Chains type bigChain hg38 color 120,20,0 visibility hide bigDataUrl grch38/t2tChm13_20200727.hg38.over.bigChain linkDataUrl grch38/t2tChm13_20200727.hg38.over.bigLink priority 3 group compGeno track grch38OverPrimaryChains parent grch38Lastz shortLabel GRCh38 Liftover Primary Chains longLabel GRCh38 LASTZ Liftover Primary Alignment Chains type bigChain hg38 color 120,0,120 visibility hide bigDataUrl grch38/t2tChm13_20200727.hg38.over-primary.bigChain linkDataUrl grch38/t2tChm13_20200727.hg38.over-primary.bigLink priority 4 group compGeno track grch38Cactus compositeTrack off shortLabel GRCh38 Cactus Pairwise longLabel GRCh38 Cactus Pairwise visibility hide priority 32 type bigChain hg38 group compGeno html needTrackDescription.html track grch38CactusAlign parent grch38Cactus shortLabel GRCh38 Cactus Alignments longLabel GRCh38 Cactus Alignments (unchained) type bigPsl color 20,120,0 visibility hide bigDataUrl grch38/GRCh38-t2tChm13_20200727.cactus.bigPsl priority 1 group compGeno track grch38CactusChaines parent grch38Cactus shortLabel GRCh38 Cactus Chained longLabel GRCh38 Cactus Chained Alignments type bigPsl color 20,120,0 visibility hide bigDataUrl grch38/GRCh38-t2tChm13_20200727.cactus.chained.bigPsl priority 2 group compGeno track grch38Synteny25kb shortLabel GRCh38 Synteny 25KB longLabel GRCh38 Synteny 25KB resolution type bigPsl color 0,20,180 visibility hide priority 40.1 bigDataUrl synteny/synteny.25kb.bigPsl group compGeno html synteny.html track grch38Synteny1mb shortLabel GRCh38 Synteny 1MB longLabel GRCh38 Synteny 1MB resolution type bigPsl color 0,20,180 visibility hide priority 41.1 bigDataUrl synteny/synteny.1mb.bigPsl group compGeno html synteny.html track uniqueRegions compositeTrack off visibility hide shortLabel Unique Regions longLabel Unique Regions Relative to GRCh38 type bigBed 4 group compGeno priority 50 track lastzUnalignedOver parent uniqueRegions shortLabel LASTZ unaligned longLabel GRCh38 LASTZ Liftover Unaligned Regions color 10,128,189 group compGeno visibility hide type bigBed 4 bigDataUrl uniqRegions/lastzUnalignedOver.bigBed priority 1 track lastzUnalignedPrimaryOver parent uniqueRegions shortLabel LASTZ Primary Unaligned longLabel GRCh38 Primary LASTZ Liftover Unaligned Regions color 10,128,189 group compGeno visibility hide type bigBed 4 bigDataUrl uniqRegions/lastzUnalignedOverPrimary.bigBed priority 2 track cactusUnaligned parent uniqueRegions shortLabel Cactus Unaligned longLabel GRCh38 Cactus Unaligned Regions color 99,128,119 group compGeno visibility hide type bigBed 4 bigDataUrl uniqRegions/cactus-unique.bigBed priority 3 track cactusUnalignedPrimary parent uniqueRegions shortLabel Cactus Unaligned Primary longLabel GRCh38 Primary Cactus Unaligned Regions color 99,128,119 group compGeno visibility dense type bigBed 4 bigDataUrl uniqRegions/cactus-unique-primary.bigBed priority 3 track cactusLastzUnaligned parent uniqueRegions shortLabel Cactus|LASTZ Unaligned longLabel GRCh38 Cactus or LASTZ Unaligned Regions color 99,128,119 group compGeno visibility hide type bigBed 4 bigDataUrl uniqRegions/cactusLastzUnaligned.bigBed priority 4 track cactusLastzUnalignedPrimary parent uniqueRegions shortLabel Cactus|LASTZ Unaligned Primary longLabel GRCh38 Primary Cactus or LASTZ Unaligned Regions color 99,128,119 group compGeno visibility dense type bigBed 4 bigDataUrl uniqRegions/cactusLastzPrimaryUnaligned.bigBed priority 3 track cactusGrch38UnplacedRandoms parent uniqueRegions shortLabel unplaced cactus longLabel GRCh38 unplaced aligned with Cactus color 10,129,182 group compGeno visibility hide type bigBed 12 bigDataUrl uniqRegions/cactus-unplaced.bigBed priority 8 track minimapGrch38UnplacedRandoms parent uniqueRegions shortLabel unplaced minimap longLabel GRCh38 unplaced aligned with Minimap2 color 10,182,129 group compGeno visibility hide type bigBed 4 bigDataUrl uniqRegions/hg38-unplaced-chm13.bigBed priority 9 ## # genes ## track transMap superTrack on shortLabel TransMap LASTZ longLabel TransMap Alignments using LASTZ chains type bigPsl priority 3 group genes track transMapEnsemblAll superTrack transMap pack shortLabel TransMap GENCODE (all chains) longLabel TransMap GENCODE Mappings using all LASTZ chains (sensitive, but not specifiec) html transMapEnsemblAll.html 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 geneName labelSeparator " " bigDataUrl transMap/t2tChm13_20200727.ensembl.transMap.all.bigPsl searchIndex name,srcTransId,geneName,geneId track transMapRefSeqAll superTrack transMap pack shortLabel TransMap RefGene (all chains) longLabel TransMap RefSeq Gene Mappings using all LASTZ chains (sensitive, but not specifiec) html transMapRefSeqAll.html 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 geneName labelSeparator " " bigDataUrl transMap/t2tChm13_20200727.refseq.transMap.all.bigPsl searchIndex name,srcTransId,geneName,geneId track refSeqBlat shortLabel RefSeq BLAT longLabel BLAT of RefSeq curated RNAs html refSeqBlat.html group genes type bigPsl priority 10.001 color 0,0,100 canPack on visibility hide baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields name,geneSym,geneId,geneType defaultLabelFields geneSym labelSeparator " " bigDataUrl refSeq-curated.bigBlatPsl searchIndex name,geneSym,geneId,geneType track gencodeBlat shortLabel GENCODE BLAT longLabel BLAT of GENCODE RNAs html gencodeBlat.html group genes type bigPsl priority 11.001 color 0,0,100 canPack on visibility hide baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields name,geneSym,geneId,geneType defaultLabelFields geneSym labelSeparator " " bigDataUrl gencode.bigBlatPsl searchIndex name,geneSym,geneId,geneType track liftOffGenes compositeTrack off visibility hide shortLabel LiftOff Genes longLabel LiftOff Genes Annotations based on GENCODE type bigGenePred group genes priority 12 track liftOffGenesAll parent liftOffGenes on bigDataUrl liftOffGenes/liftOffGenes.all.bigGenePred shortLabel LiftOff Genes (All) longLabel LiftOff Genes - all annotations type bigGenePred group genes labelFields name, name2 defaultLabelFields name searchIndex name,name2 track liftOffGenesOrf parent liftOffGenes on bigDataUrl liftOffGenes/liftOffGenes.orf_only.bigGenePred shortLabel LiftOff Genes (ORFs) longLabel LiftOff Genes - annotations with ORFs type bigGenePred group genes labelFields name, name2 defaultLabelFields name searchIndex name,name2 ## # Expression ## track shortRnaSeqIntrons shortLabel Short RNA-Seq Introns longLabel Short RNA-Seq Introns from ENCODE group rna visibility hide type bigBed 12 itemRgb on maxItems 100000 bigDataUrl shortRnaSeqIntrons.bigBed priority 3 track proSeq compositeTrack off visibility hide shortLabel PRO-seq longLabel PRO-Seq group rna priority 4 track proSeqPos parent proSeq on shortLabel PRO-seq positive longLabel PRO-Seq positive strand group rna autoScale on negateValues off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 type bigWig 0 100 bigDataUrl proSeq/proSeq-pos.bigWig priority 1 track proSeqNet parent proSeq on shortLabel PRO-seq negative longLabel PRO-Seq negative strand group rna autoScale on negateValues on maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 type bigWig 0 100 bigDataUrl proSeq/proSeq-neg.bigWig priority 2 ## # Cactus & CAT ## include CAT/trackDb.txt