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/egapx.html src/hg/makeDb/trackDb/contrib/bTaeGut7/egapx.html new file mode 100644 index 00000000000..a68a68bcb70 --- /dev/null +++ src/hg/makeDb/trackDb/contrib/bTaeGut7/egapx.html @@ -0,0 +1,76 @@ +<h2>Description</h2> +<p> +This track is part of the <a href="hgTrackUi?db=$db&g=$parentTrack&hgsid=$hgsid">Genes and Retrocopies</a> collection of the zebra finch telomere-to-telomere hub. +</p> +<p> +This track shows protein-coding and long non-coding RNA gene models built by NCBI's +eukaryotic genome annotation pipeline. Models are constructed from alignments of RNA +sequencing reads and of proteins from related species, combined with ab initio prediction, so +each transcript reflects both direct expression evidence and similarity to known genes. The +track contains about 142,000 transcripts. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Transcripts are drawn in the standard gene model style: boxes for exons, thin lines with +arrowheads for introns showing the direction of transcription, and thicker boxes for the +coding part of each exon. Clicking a transcript opens a page with its identifier and +structure. +</p> + +<h2>Methods</h2> +<p> +Both haplotypes were annotated with the public version of NCBI's Eukaryotic Genome Annotation +Pipeline, EGAPx v0.4.1 (<a href="https://github.com/ncbi/egapx" target="_blank">github.com/ncbi/egapx</a>), which combines RNA-seq and protein alignments with ab initio +modelling. A set of 33 Illumina RNA-seq datasets covering a range of tissues and developmental +stages was used, drawn in part from NCBI BioProjects PRJNA1032078, PRJNA516733 and +PRJNA977995. Curated RefSeq and RNA-seq supported model RefSeq proteins from human, chicken, +song sparrow, barn swallow and other sauropsids provided additional support, and one-to-one +orthologs of human protein-coding genes were computed from protein homology and local synteny. +</p> +<p> +The file was taken from GenomeArk at <a href="https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/genes/bTaeGut7v0.4_MT_rDNA.EGAPx.v0.1.gtf.gz" target="_blank">https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/genes/bTaeGut7v0.4_MT_rDNA.EGAPx.v0.1.gtf.gz</a>. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. +The GTF was converted to a genePred with gtfToGenePred and then to bigGenePred, so exon +structure and coding boundaries are preserved. The conversion, and the whole hub, is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC kent source tree. +</p> + +<h2>Data Access</h2> +<p> +The data can be explored interactively in table format with the +<a href="../cgi-bin/hgTables">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or +tab-separated tables. From scripts, the data can be accessed through our +<a href="https://api.genome.ucsc.edu" target="_blank">API</a>, track=<i>egapx</i>. +</p> + +<p> +For automated download and analysis, this annotation is a bigBed file inside the hub. Individual +regions or the whole annotation can be obtained with <tt>bigBedToBed</tt>, which can be compiled from +source or downloaded as a precompiled binary; instructions are +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +The tool also fetches a range, for example +<tt>bigBedToBed <hubUrl>/GCF_048771995.1/egapx.bb -chrom=NC_133024.1 -start=0 -end=100000 stdout</tt>, +where <hubUrl> is the directory this hub was loaded from. +</p> +<p> +The original annotation files are on GenomeArk, <a href="https://genomeark.s3.amazonaws.com/index.html?prefix=species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/" target="_blank">in the bTaeGut7 annotations directory</a>. +</p> + +<h2>References</h2> +<p> +Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, +Chen Y <em>et al</em>. +<a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(26)00816-0" target="_blank"> +The complete genome of a songbird</a>. +<em>Cell</em>. 2026 Aug 6;189(16):4922-4945.e12. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/42561917" target="_blank">42561917</a> +</p> + +<h2>Credits</h2> +<p> +The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at +The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to +Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before +and after publication. The analysis code is at <a href="https://github.com/gf777/T2T-zebra-finch" target="_blank">github.com/gf777/T2T-zebra-finch</a>. This hub was assembled at UCSC from the IGV +session distributed with the annotations, using hubtools. +</p>