e6d1189bea4cc541396f842b65a3392c33c8e734 max Wed Sep 2 02:55:03 2026 -0700 hprc2annot: put the collection in git and fix the QA findings The HPRC Release 2 GenArk contributed track collection (7 tracks x 462 assemblies) had only its one-line betaGenArk.txt enable checked in. Add the makeDoc, the build scripts, the seven track description pages and the trackDb stanzas, and fix the problems QA found. Data fixes, both rebuilt across all 462 assemblies: - liftoff: gff3ToGenePred was naming each genePred after the gene, so every transcript of a gene shared one name, the RefSeq accession was lost and the transcript_biotype lookup never matched (type empty on 99.8% of rows). Pass -rnaNameAttr=ID. Duplicate (chrom,start,end,name) tuples go from 24,969 to 0 and type is now empty on 2,132 of 82,973,730 rows. The same flag is a no-op on the CAT GFF3 (byte-identical output), so both gene tracks now share one code path and CAT needs no rebuild. - segdups: the build read SEDEF column 6, strand1, which is "+" by construction on every row, so every inverted duplication rendered forward. Use column 14, strand2, the orientation of the paralogous copy: 13.8M + and 13.8M - across the collection. Also translate the paralog partner out of PanSN through the GenArk chromAlias, since the browser does not translate a plain text field, and store identity as a percentage so the mouseover can read it. hprc2annotFixBed.sh is not idempotent for pclai: a second run re-parses an already-parsed name and blanks the values. It now refuses to touch a converted file. GCA_041900255.1 was damaged that way and is rebuilt from source. Provenance, all from the QA report: - stats.tsv is appended to rather than truncated on every run, and each run regenerates log/summary.tsv, a per-track roll-up over the collection. - dataVersion on all seven tracks. - Rows are now dropped for exactly two reasons and both are counted: past the end of the sequence, or a sequence name absent from the assembly, which also warns with example names. Only GCA_018472765.3 trips the second, the known upstream contig-version mismatch. genePredToBigGenePred failure is checked and an empty conversion result is a failure, not a valid empty bigBed. Description pages: fix a raw UTF-8 character, rewrite the segdups and pclai display conventions which still described the data before the name field was blanked, add a color legend checked against the data, add the pcLAI preprint (from the Crossref record, since it has no PMID), and correct the stated reason liftoff drops transcripts. Display: title case on the short labels, "Active centromeres" shortened to fit the 17-character limit, pcLAI to pack since it has no readable dense state, liftoff and segdups to dense, and a filter on the segdups original flag. refs #35415 diff --git src/hg/makeDb/trackDb/contrib/hprc2annot/censatCentromeres.html src/hg/makeDb/trackDb/contrib/hprc2annot/censatCentromeres.html new file mode 100644 index 00000000000..dd1c271870b --- /dev/null +++ src/hg/makeDb/trackDb/contrib/hprc2annot/censatCentromeres.html @@ -0,0 +1,63 @@ +<h2>Description</h2> +<p> +This track shows the active centromere region of each chromosome in this Human +Pangenome Reference Consortium (HPRC) Release 2 assembly. The centromere is the +constricted part of a chromosome where the two copies are held together and where +the spindle attaches to pull them apart during cell division. Within the large +satellite arrays of each chromosome, one region carries the specialized chromatin +that actually recruits this machinery; that region is the "active" centromere +shown here. This is a summarized companion to the more detailed centromere +satellite (cenSat) track. +</p> + +<h2>Display Conventions</h2> +<p> +Each item is the active centromere interval on one sequence, drawn as a simple +block. There are no sub-features. +</p> + +<h2>Methods</h2> +<p> +Active centromere regions were derived from the cenSat annotation of each +complete assembly, following the approach developed for the telomere-to-telomere +CHM13 reference (see reference below). +</p> +<p> +The annotation files were obtained from the HPRC Release 2 data collection on the +public <tt>s3://human-pangenomics</tt> bucket, indexed at +<a href="https://github.com/human-pangenomics/hprc_intermediate_assembly/tree/main/data_tables/annotation/censat" target="_blank">the hprc_intermediate_assembly data tables</a>. +Each per-assembly BED file was converted to a UCSC bigBed file. The steps are described in the +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/contrib/hprc2annot.txt" target="_blank">makeDoc</a>, +the build scripts are in the +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/hprc2annot" target="_blank">kent source tree</a>, +and the track configuration is in +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/trackDb/contrib/hprc2annot" target="_blank">trackDb/contrib/hprc2annot</a>. +</p> + +<h2>Data Access</h2> +<p> +For automated analysis, the annotation is stored in a bigBed-format file +(<tt>censatCentromeres.bb</tt>) that can be read with the UCSC tool +<tt>bigBedToBed</tt>. The original files are available from the HPRC S3 bucket +linked above. +</p> + +<h2>Credits</h2> +<p> +Annotations were generated by the Human Pangenome Reference Consortium. Thanks to +the HPRC production team for making these data available. +</p> + +<h2>References</h2> + + +<p> +Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov +FD, Shew CJ <em>et al</em>. +<a href="https://www.science.org/doi/10.1126/science.abl4178" target="_blank"> +Complete genomic and epigenetic maps of human centromeres</a>. +<em>Science</em>. 2022 Apr;376(6588):eabl4178. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35357911" target="_blank">35357911</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233505/" target="_blank">PMC9233505</a> +</p> +