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/censat.html src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html index 599bff30b54..28576c83e7e 100644 --- src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html +++ src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html @@ -1,71 +1,71 @@ <h2>Description</h2> <p> This track shows the centromere satellite (cenSat) annotation for this Human Pangenome Reference Consortium (HPRC) Release 2 assembly. Centromeres and other heterochromatic regions of human chromosomes are built largely from <i>satellite DNA</i>: long stretches of short sequences repeated head to tail millions of times. These regions are where the cell's machinery attaches during cell division, and until complete (telomere-to-telomere) assemblies became available they could not be sequenced or annotated. This track labels the different families of satellite repeat along each sequence, including the alpha satellite higher-order repeats that define the active centromere. </p> <h2>Display Conventions</h2> <p> Each item is one satellite region, labeled with its repeat class (for example alpha-satellite higher-order repeat, monomeric alpha satellite, or one of the human satellite families HSat1/2/3). Items are colored by the standard cenSat annotation color scheme, so that the different satellite families can be told apart at a glance; the specific family is given in the item name and on the details page. The repeat-class name is searchable. </p> <h2>Methods</h2> <p> The cenSat annotation identifies and classifies satellite arrays in a complete assembly, combining alpha-satellite higher-order-repeat detection with a repeat-family classification of the remaining satellite sequence, 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 cenSat BED file was converted to a UCSC bigBed file, preserving the item colors. 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>censat.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. 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> 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>