c3bb4e5212585dc21a7e4f23db0978287ced674b lrnassar Fri Jun 7 17:41:14 2024 -0700 Releasing the latest GENCODE versions track, refs #33082 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 6909a8f..7b3c37a 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,66 @@ </div> <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 <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 <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="060724"></a> +<h2>June 7, 2024 New GENCODE gene tracks: Human V46 (hg19/hg38) - Mouse M35 +(mm39)</h2> +<p> +We are pleased to announce new GENCODE Gene annotation tracks, which correspond +to <a href="https://www.ensembl.info/2024/05/13/ensembl-112-has-been-released/" +target="_blank">Ensembl 112</a>, for three assemblies: <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV46lift37">hg19/GRCh37</a>, +<a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=wgEncodeGencodeV46">hg38/GRCh38</a>, +and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM35">mm39/GRCm39</a>. +For human, the GENCODE V46 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 Lou Nassar for the development and +release of these tracks.</p> + <a name="052224"></a> <h2>May. 22, 2024 New GENCODE "KnownGene" V46 for human (hg38) and VM35 for mouse (mm39)</h2> <p> We are pleased to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&g=knownGene&c=chrX">GENCODE V46 (hg38)</a> and the <a href="/cgi-bin/hgTrackUi?db=mm39&g=knownGene&c=chrX">GENCODE VM35 (mm39)</a> gene tracks. The GENCODE "KnownGene" V46 and VM35 gene tracks were built using a UCSC pipeline (KnownGene) and the GENCODE comprehensive gene set to generate high-quality manual annotations merged with evidence-based automated annotations. The GENCODE "KnownGene" tracks are our default gene tracks, which have extensive associations to external sources. This allows for additional metadata on every item as well as external links. The track description pages contain options for configuring the display, such as showing non-coding genes, splice variants, and pseudogenes.</p>