0f899681f739d9ea4d7b4b7a5d7730a92e3c8c7b Merge parents 9e6cf35 809d9dc dschmelt Tue Feb 11 13:54:08 2020 -0800 Announcing ncbi refSeq update, fixing merge refs #24604 diff --cc src/hg/htdocs/goldenPath/newsarch.html index df7f1fe,164712c..5bae14b --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@@ -40,32 -40,68 +40,68 @@@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> + <a name="021120"></a> + <h2>Feb. 11, 2020 New GENCODE gene tracks: Human V33 (hg19/hg38) - Mouse M24 + (mm10)</h2> + <p> + We are pleased to announce new GENCODE Gene annotation tracks, which correspond + to <a href="http://www.ensembl.info/2019/10/17/whats-coming-up-in-ensembl-release-99/" + target="_blank">Ensembl 99</a>, for three assemblies: <a target="_blank" + href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV33lift37">hg19/GRCh37</a>, + <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38c=chr1&g=wgEncodeGencodeV33">hg38/GRCh38</a>, + and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm10&c=chr12&g=wgEncodeGencodeVM24">mm10/GRCm38</a>. + For human, the GENCODE V33 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 mm10 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="020720b"></a> -<h2>Feb. 7 2020 Updated data for NCBI RefSeq tracks for human assemblies hg19 +<a name="021020"></a> +<h2>Feb. 10 2020 Updated data for NCBI RefSeq tracks for human assemblies hg19 and hg38</h2> <p> We are happy to release the updated NCBI RefSeq Annotation Release 109.20190905 track on the Genome Browser. The NCBI RefSeq Genes composite track shows human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). This update adds more than 500 new gene entries to the collection of nearly 167,000 annotations. More information can be found on the track description pages for these composite tracks for <a href="../../cgi-bin/hgTrackUi?db=hg19&g=refSeqComposite">hg19</a> and <a href="../../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite">hg38</a>.</p> <p> We would like to thank NCBI and the RefSeq Annotation database for collecting and curating this data. We would also like to thank Hiram Clawson and Daniel Schmelter for their role creating, documenting, and reviewing these tracks.</p>