c5ce282587dbf8ec6a7b28470e0449ca6af9e250 gperez2 Fri Nov 8 15:24:16 2024 -0800 Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index b9f1602..d23eddc 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,69 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> + +<a name="110824"></a> +<h2>Nov. 8, 2024 New GENCODE gene tracks: Human V47 (hg19/hg38) - Mouse M36 +(mm39)</h2> +<p> +We are pleased to announce new GENCODE Gene annotation tracks, which correspond +to <a href="https://www.ensembl.info/2024/10/18/ensembl-113-has-been-released/" +target="_blank">Ensembl 113</a>, for three assemblies: <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV47lift37">hg19/GRCh37</a>, +<a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=wgEncodeGencodeV47">hg38/GRCh38</a>, +and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM36">mm39/GRCm39</a>. +For human, the GENCODE V47 annotations were mapped to hg38/GRCh38 and then back-mapped +to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following +tracks:</p> +<ul> + <li>Basic - a subset of the <em>Comprehensive set</em>.</li> + <li>Comprehensive - all GENCODE coding and non-coding transcript annotations, including + polymorphic pseudogenes. This includes both manual and automatic annotations.</li> + <li>Pseudogenes - all annotations except polymorphic pseudogenes.</li></ul> +<p> +The hg38 and mm39 assemblies also include the following tracks that are not available on hg19: +</p> +<ul> + <li>2-way Pseudogenes - pseudogenes predicted by both the Yale Pseudopipe and UCSC + Retrofinder pipelines.</li> + <li>PolyA - polyA signals and sites manually annotated on the genome based on transcribed + evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the + genome.</li></ul> +<p> +Details on each release can be found on the <a target="_blank" +href="https://www.gencodegenes.org/">GENCODE site</a>. This includes <a target="_blank" +href="https://www.gencodegenes.org/human/stats.html">statistics on each release</a>. +<p>We would like to thank the <a target="_blank" +href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these +annotations. We would also like to thank Mark Diekhans and Gerardo Perez for the development and +release of these tracks.</p> + + + <a name="110424"></a> <h2>Nov. 4, 2024 GIAB Problematic Regions tracks for human (hg38 and hs1)</h2> <p> We are pleased to announce the release of the <a href="https://www.nist.gov/programs-projects/genome-bottle" target="_blank" >Genome in a Bottle (GIAB)</a> Problematic Regions tracks for the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=problematicGIAB" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=hub_3671779_hs1&position=default&g=hub_3671779_problematic" target="_blank">hs1</a> human assemblies. The tracks provide stratifications of the genome to evaluate variant calls in complex regions and it is designed for use with Global Alliance for Genomic Health (GA4GH) benchmarking tools like <a href="https://github.com/Illumina/hap.py" target="_blank">hap.py</a>. It includes regions with low complexity, segmental duplications, functional regions, and difficult-to-sequence areas. The GIAB Problematic Regions composite track consists of four subtracks:</p>