1682366b1827b7559f8e1e41635acff6c5ea15e9 max Wed Sep 9 06:05:05 2026 -0700 hprc2annot: move the makeDoc into its own directory and repoint the links The makeDoc has grown a companion (an hg38 pcLAI doc is in progress), so it moves from doc/contrib/hprc2annot.txt into doc/contrib/hprc2annot/, matching how the scripts and trackDb copies are already laid out. The file itself gains a section on the pcLAI scatterplot on the details page: where the reference panel comes from, the four ancestry centroids the discretized field takes across the release, and why the file is read through hgTrackUi rather than fetched by the browser. All seven track description pages linked to the old flat path and would have 404'd, so they are repointed. Six of them change only that link; pclai.html has further edits still in progress and keeps its own copy of the change. refs #35415 diff --git src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html index 1845dea164b..9d634359a66 100644 --- src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html +++ src/hg/makeDb/trackDb/contrib/hprc2annot/catGenes.html @@ -1,78 +1,78 @@ <h2>Description</h2> <p> This track shows gene annotations produced by the Comparative Annotation Toolkit (CAT) for this Human Pangenome Reference Consortium (HPRC) Release 2 assembly. Genes are the stretches of DNA that are copied into RNA and, for most of them, translated into protein. Because each pangenome assembly is a newly sequenced human genome, its genes are not known in advance; CAT infers them by carrying a well-studied reference annotation across a whole-genome alignment onto the new assembly, and by combining that projection with direct transcript evidence. The result is a consistent set of gene models for every assembly, which makes it possible to compare the same gene across many individuals. </p> <h2>Display Conventions</h2> <p> Genes follow the standard UCSC gene display: boxes are exons, connecting lines are introns, and arrows on the introns show the direction of transcription. Thicker boxes mark the coding portion (CDS) and thinner boxes the untranslated regions (UTRs). Where the browser is zoomed in far enough, the amino-acid translation and, on request, the underlying bases are shown. Items are labeled by gene name where a name was available from the reference; the transcript identifier and the gene and transcript biotypes are shown on the item details page. Both gene name and transcript identifier are searchable. </p> <h2>Methods</h2> <p> The Comparative Annotation Toolkit projects an existing high-quality reference annotation onto a target genome through a whole-genome (Cactus/progressiveCactus) alignment, reconciles the projected transcripts with <i>ab initio</i> and transcript-based evidence, and produces a filtered consensus gene set with stable cross-assembly identifiers. See the reference below for the full algorithm. For the HPRC pangenome, CAT was run against the CHM13/GRCh38-based reference annotation to annotate each assembly. </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/cat" target="_blank">the hprc_intermediate_assembly data tables</a>. Each per-assembly GFF3 was converted to a UCSC bigGenePred file with <tt>gff3ToGenePred</tt> and <tt>genePredToBigGenePred</tt>; gene symbols and gene and transcript biotypes from the GFF3 were carried into the display fields. 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>, +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/contrib/hprc2annot/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>catGenes.bb</tt>) that can be read with the UCSC tool <tt>bigBedToBed</tt>, which can be compiled from source or downloaded as a precompiled binary. It can also extract features for a region, for example: <tt>bigBedToBed catGenes.bb -chrom=CM085953.1 -start=0 -end=100000 stdout</tt>. The original annotation 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> Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE <em>et al</em>. <a href="http://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=29884752" target="_blank"> Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation</a>. <em>Genome Res</em>. 2018 Jul;28(7):1029-1038. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29884752" target="_blank">29884752</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028123/" target="_blank">PMC6028123</a> </p>