a8694a3b22d43f0536c02101e9f3b56b5339b4dc max Wed Sep 9 05:47:17 2026 -0700 hubtools: add "import igv" and "splitHap", and the bTaeGut7 zebra finch hub import igv builds a hub from an IGV session XML. Every Track element becomes a track, in session order, with the IGV display attributes translated to trackDb settings. Files the browser can read over the network are linked where they are; bed, gff, gtf, wig and bedGraph are downloaded and converted, which needs chrom.sizes and gets them from --chromSizes, from the UCSC assembly, or from a bigWig of the session itself, the only source there is for a custom assembly. The BED cleaner exists because real files are not to spec: reversed start/end, scores over 1000, "#rrggbb" colours, names past 255 characters, and columns that are not the BED field they sit in, such as trf writing the repeat motif where thickStart belongs. splitHap turns a hub built on a diploid assembly into one hub with a genome per haplotype, reading both assemblies' chrom.sizes and chromAlias from GenArk and sending each record to whichever assembly has its sequence. It writes splitHap.report.txt with the records per track per haplotype, the sequences neither assembly has, and the records reaching past a sequence end, and checks every track as it goes: records read must equal records matched plus records with no sequence, and every match must produce an output record or a drop. A track that does not add up stops the run rather than being written up as a finding. Two conversion fixes that came out of the zebra finch data. GFF3 requires unique IDs, but an annotation of a phased assembly often gives both haplotypes the same ID; gff3ToGenePred then merges the two copies into one transcript spanning two chromosomes and discards it, which was losing 31 of 182 retrocopies. IDs that occur on more than one sequence are now made unique per sequence first. And a feature name is now taken from the first non-numeric attribute, so a RepeatMasker GFF gives Motif:Tgut716A rather than the running number in ID=. genark addContrib gains --tier alpha|beta|public. It edits only betaGenArk.txt and publicGenArk.txt; beta.hub.txt and public.hub.txt are generated from those lists and shipped by quickPush.pl, so writing them by hand would push content outside the normal flow and lose it at the next clade build. The default alpha tier leaves the lists untouched, so re-running an install cannot demote a collection that is already promoted. doc/contrib/bTaeGut7 and trackDb/contrib/bTaeGut7 are the zebra finch telomere-to-telomere hub built with the above, from the IGV session the authors ship with the annotations on GenomeArk (Formenti et al, Cell 2026, PMID 42561917). 21 tracks in 6 collections plus 3 standalone, 27 description pages, and a makeDoc recording where every record went. diff --git src/hg/makeDb/trackDb/contrib/bTaeGut7/bTaeGut7.trackDb.txt src/hg/makeDb/trackDb/contrib/bTaeGut7/bTaeGut7.trackDb.txt new file mode 100644 index 00000000000..5de4ecdbe18 --- /dev/null +++ src/hg/makeDb/trackDb/contrib/bTaeGut7/bTaeGut7.trackDb.txt @@ -0,0 +1,292 @@ +track gcPercent +shortLabel GC Content +longLabel GC content in 200 bp windows +type bigWig +bigDataUrl gcPercent.bw +visibility full +priority 1.1 +group map +html gcPercent.html +autoScale on +viewLimits 0:63.03 +graphTypeDefault points +windowingFunction mean + +track seqEntropy +shortLabel Sequence Entropy +longLabel Shannon sequence entropy in 200 bp windows +type bigWig +bigDataUrl seqEntropy.bw +visibility full +priority 1.2 +group map +html seqEntropy.html +autoScale on +viewLimits 0:1.99 +graphTypeDefault points +windowingFunction mean + +track nonBdna +shortLabel Non-B DNA +longLabel Non-B DNA motifs: G-quadruplexes, Z-DNA, triplex and repeat-based structures +type bigBed 9 +bigDataUrl nonBdna.bb +visibility dense +priority 1.3 +group varRep +html nonBdna.html +itemRgb on +maxWindowToDraw 26799200 + +track readCoverage +superTrack on show +shortLabel Read Coverage +longLabel Long-read sequencing coverage +priority 2 +group map +html readCoverage.html + + track covHifi + parent readCoverage + shortLabel HiFi Coverage + longLabel PacBio HiFi read coverage + type bigWig + bigDataUrl covHifi.bw + visibility full + priority 2.1 + html covHifi.html + autoScale on + viewLimits 0:240.128 + graphTypeDefault bar + windowingFunction mean + + track covOnt + parent readCoverage + shortLabel ONT Coverage + longLabel Oxford Nanopore read coverage + type bigWig + bigDataUrl covOnt.bw + visibility full + priority 2.2 + html covOnt.html + autoScale on + viewLimits 0:290.112 + graphTypeDefault bar + windowingFunction mean + + track covClr + parent readCoverage + shortLabel CLR Coverage + longLabel PacBio CLR read coverage from the earlier bTaeGut1.4 individual + type bigWig + bigDataUrl covClr.bw + visibility full + priority 2.3 + html covClr.html + autoScale on + viewLimits 0:562.551 + graphTypeDefault bar + windowingFunction mean + +track genes +superTrack on show +shortLabel Genes and Retrocopies +longLabel Gene models and processed retrocopies +priority 3 +group genes +html genes.html + + track egapx + parent genes + shortLabel EGAPx Genes + longLabel Protein-coding and lncRNA gene models from NCBI EGAPx + type bigGenePred + bigDataUrl egapx.bb + visibility pack + priority 3.1 + html egapx.html + + track retrocopies + parent genes + shortLabel Retrocopies + longLabel Processed retrocopies identified with RCPedia + type bigGenePred + bigDataUrl retrocopies.bb + visibility pack + priority 3.2 + html retrocopies.html + +track repeats +superTrack on show +shortLabel Repeats +longLabel Transposable elements, tandem repeats and satellite arrays +priority 4 +group varRep +html repeats.html + + track transposons + parent repeats + shortLabel Transposable Elements + longLabel Transposable elements and interspersed repeats from EDTA2 + type bigBed 9 + + bigDataUrl transposons.bb + visibility dense + priority 4.1 + html transposons.html + maxWindowToDraw 809629799 + itemRgb on + + track tandemRepeats + parent repeats + shortLabel Tandem Repeats + longLabel Tandem repeat arrays from Tandem Repeats Finder + type bigBed 6 + + bigDataUrl tandemRepeats.bb + visibility dense + priority 4.2 + html tandemRepeats.html + maxWindowToDraw 11605447 + + track satellome + parent repeats + shortLabel Satellite Repeats + longLabel Satellite repeat arrays from the Satellome catalog + type bigBed 6 + bigDataUrl satellome.bb + visibility pack + priority 4.3 + html satellome.html + +track centroTelo +superTrack on show +shortLabel Centromeres and Telomeres +longLabel Centromere cores and markers, telomeres and interstitial telomeric sequences +priority 5 +group map +html centroTelo.html + + track centroSat + parent centroTelo + shortLabel Centromeric Satellites + longLabel Centromeric satellite arrays from a curated satellite library + type bigBed 9 + + bigDataUrl centroSat.bb + visibility pack + priority 5.1 + html centroSat.html + itemRgb on + + track centroCores + parent centroTelo + shortLabel Centromere Cores + longLabel Centromere core regions predicted by Centromere Detector + type bigBed 9 + + bigDataUrl centroCores.bb + visibility pack + priority 5.2 + html centroCores.html + itemRgb on + + track centroMarkers + parent centroTelo + shortLabel Centromere Markers + longLabel Mapped positions of published centromeric and distal primer pairs + type bigBed 4 + bigDataUrl centroMarkers.bb + visibility pack + priority 5.3 + html centroMarkers.html + + track telomeres + parent centroTelo + shortLabel Telomeres + longLabel Terminal TTAGGG telomere arrays + type bigBed 4 + + bigDataUrl telomeres.bb + visibility pack + priority 5.4 + html telomeres.html + + track itsRepeats + parent centroTelo + shortLabel Interstitial Telomeres + longLabel Interstitial telomeric sequences away from the chromosome ends + type bigBed 3 + bigDataUrl itsRepeats.bb + visibility pack + priority 5.5 + html itsRepeats.html + +track structVar +superTrack on show +shortLabel Structural Variation +longLabel Previously unassembled regions and large inter-haplotype variants +priority 6 +group varRep +html structVar.html + + track newRegions + parent structVar + shortLabel Previously Unassembled + longLabel Regions missing or collapsed in the earlier bTaeGut1.4 reference + type bigBed 3 + bigDataUrl newRegions.bb + visibility pack + priority 6.1 + html newRegions.html + + track largeSv + parent structVar + shortLabel Large SVs + longLabel Large structural variants between the maternal and paternal haplotypes + type bigBed 4 + bigDataUrl largeSv.bb + visibility pack + priority 6.2 + html largeSv.html + +track chromatin +superTrack on show +shortLabel Methylation and 3D Chromatin +longLabel CpG methylation and Hi-C A/B compartments +priority 7 +group regulation +html chromatin.html + + track methyl5mC + parent chromatin + shortLabel 5mC Methylation + longLabel CpG 5-methylcytosine probability from PacBio HiFi reads + type bigWig + bigDataUrl methyl5mC.bw + visibility full + priority 7.1 + html methyl5mC.html + autoScale on + viewLimits 0:94.529 + graphTypeDefault bar + windowingFunction mean + + track compartE1 + parent chromatin + shortLabel Compartment E1 + longLabel Hi-C first eigenvector at 200 kb, positive in the active A compartment + type bigWig + bigDataUrl compartE1.bw + visibility full + priority 7.2 + html compartE1.html + autoScale on + viewLimits -1.143:1.67 + windowingFunction mean + + track compartAB + parent chromatin + shortLabel A/B Compartments + longLabel Hi-C A and B compartment intervals at 200 kb + type bigBed 9 + bigDataUrl compartAB.bb + visibility dense + priority 7.3 + html compartAB.html + itemRgb on