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/nonBdna.html src/hg/makeDb/trackDb/contrib/bTaeGut7/nonBdna.html new file mode 100644 index 00000000000..bfaff55319f --- /dev/null +++ src/hg/makeDb/trackDb/contrib/bTaeGut7/nonBdna.html @@ -0,0 +1,107 @@ +<h2>Description</h2> +<p> +Most DNA in a cell is the familiar right-handed B-form double helix, but particular sequences +can fold into other shapes: four-stranded G-quadruplexes, left-handed Z-DNA, hairpins formed +by inverted repeats, and three-stranded triplexes. These structures can stall replication and +transcription, they are associated with elevated mutation rates, and they are enriched in +exactly the regions that were hardest to assemble. This track shows 11.3 million predicted +motifs in eight classes. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Each motif is drawn in the color of its class. The class, the motif length and the sequence +signature are in the item name and on the details page. +</p> +<table class="stdTbl"> + <tr><th style="background-color:#DB5829;width:2em"> </th> + <td>G4, G-quadruplex predicted by Quadron</td></tr> + <tr><th style="background-color:#894B45;width:2em"> </th> + <td>Z, Z-DNA forming motif</td></tr> + <tr><th style="background-color:#AE75A2;width:2em"> </th> + <td>APR, A-phased repeat</td></tr> + <tr><th style="background-color:#7BB0DF;width:2em"> </th> + <td>DR, direct repeat</td></tr> + <tr><th style="background-color:#E9E66D;width:2em"> </th> + <td>IR, inverted repeat, able to form a cruciform</td></tr> + <tr><th style="background-color:#F4A637;width:2em"> </th> + <td>MR, mirror repeat</td></tr> + <tr><th style="background-color:#ED952C;width:2em"> </th> + <td>TRI, triplex-forming motif, extracted from the mirror repeats</td></tr> + <tr><th style="background-color:#008A69;width:2em"> </th> + <td>STR, short tandem repeat</td></tr> +</table> +<p> +Because there are more than eleven million motifs, the track is set to dense by default and +stops drawing above the window size inherited from the original session. Zoom in to see +individual motifs. +</p> + +<h2>Methods</h2> +<p> +A-phased repeats, direct repeats, inverted repeats, mirror repeats, short tandem repeats and +Z-DNA motifs were annotated with gfa. Triplex motifs were marked by gfa and extracted from the +mirror repeat set. G-quadruplexes were predicted with Quadron; predictions with a score of NA +were removed, which Quadron produces for sequence within 50 bp of the end of an input +sequence, typically one or two motifs per chromosome. +</p> +<p> +The file was taken from GenomeArk at <a href="https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/nonB/bTaeGut7v0.4_MT_rDNA.gfa%2BQuadron.sorted.v0.1.bed" target="_blank">https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/nonB/bTaeGut7v0.4_MT_rDNA.gfa%2BQuadron.sorted.v0.1.bed</a>. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. 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>nonBdna</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/nonBdna.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> +<p> +Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/21097885" target="_blank"> +Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes</a>. +<em>Nucleic Acids Res</em>. 2011 Jan;39(Database issue):D383-91. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21097885" target="_blank">21097885</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013731/" target="_blank">PMC3013731</a> +</p> +<p> +Sahakyan AB, Chambers VS, Marsico G, Santner T, Di Antonio M, Balasubramanian S. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/29109402" target="_blank"> +Machine learning model for sequence-driven DNA G-quadruplex formation</a>. +<em>Sci Rep</em>. 2017 Nov 6;7(1):14535. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29109402" target="_blank">29109402</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673958/" target="_blank">PMC5673958</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>