a5b92d53906ac006cb6508dcd1efdda70b2196e2 gperez2 Fri Nov 8 16:27:19 2024 -0800 Updating the newsarch for the hg38, hg19 (V47), and mm39 (VM36) All GENCODE release. refs #34215 #34214 #34217 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d23eddc..b99d9bf 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -59,53 +59,53 @@ <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 +We are happy 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: +The hg38 and mm39 assemblies also include the following track that is 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 + <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> + 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