00edcd80bade80a533d5392af0106ab36daffd4f gperez2 Thu Aug 17 17:15:41 2023 -0700 Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #30837 #30838 #30839 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 00ddc48..70594a7 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,74 @@ </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> <!-- ============= 2023 archived news ============= --> <a name="2023"></a> +<a name="081823"></a> +<h2>Aug. 18, 2023 New GENCODE gene tracks: Human V44 (hg19/hg38) - Mouse VM33 +(mm39)</h2> +<p> +We are pleased to announce new GENCODE Gene annotation tracks, which correspond +to <a href="https://www.ensembl.info/2023/07/17/ensembl-110-has-been-released/" +target="_blank">Ensembl 110</a>, for three assemblies: <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=wgEncodeGencodeV44lift37">hg19/GRCh37</a>, +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=wgEncodeGencodeV44">hg38/GRCh38</a>, +and +<a target="_blank" href="/cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM33">mm39/GRCm39</a>. +For human, the GENCODE V44 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 track that is not available on hg19: +</p> +<ul> + <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> +<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="080723"></a> <h2>Aug. 07, 2023 Introducing an interactive tutorial for the UCSC Genome Browser</h2> <p> We are happy to announce the release of a new interactive tutorial for the UCSC Genome Browser. The tutorial is designed to help new users navigate the UCSC Genome Browser. Topics such as navigating around the Genome Browser display, configuring track display settings, searching for tracks, and viewing the negative strand (3' to 5') are covered in the tutorial.</p> <p> To begin the tutorial, select the <em>Interactive tutorial</em> from the "Help" drop-down menu. <div class="text-center"> <a href="/cgi-bin/hgTracks?db=hg38&position=default"> <img src="/images/newsArchImages/hgTracksTutorial.png" width="900"> </a> </div>