72aab260adeca9c17571ae509c84bad9bbe7e9ce dschmelt Tue Jul 20 12:09:35 2021 -0700 Announcing GENCODE refs #27785 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 87673c5..a6494ba 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,59 @@ <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> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="072021"></a> +<h2>July 20, 2021 Updated GENCODE tracks released for hg38, hg19, and mm39</h2> +<p> +We have updated our GENCODE gene datasets to the latest releases; v38 +for human (hg38 & hg19) and v27 for the mouse genome assembly (mm39). +These new annotation data were released by GENCODE in May 2021 +and correspond to the Ensembl Genes 104 dataset. +</p> +<p> +These tracks can be found in our All GENCODE super-track folder, +with subset tracks and abundant filter options. This super-track +contains many previous versions of the GENCODE genes for easy +comparison. From the +<a href="https://www.gencodegenes.org/human/stats.html"> +GENCODE stats page</a>, +this updated dataset has approximately 60.6k genes and 237k transcripts on +the human hg38 assembly.</p> +<p> +For more information or to visualize the data, +you can visit the following track description pages:</p> +<ul> +<li><a href="../../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV38"> +All GENCODE v38 for hg38</a></li> +<li><a href="../../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV38lift37"> +GENCODE lifted Annotations V38lift37 for hg19</a></li> +<li><a href="../../cgi-bin/hgTrackUi?db=mm39&g=wgEncodeGencodeVM27"> +All GENCODE annotations VM27 for mm39</a></li> +</ul> + <a name="071421"></a> <h2>July 14, 2021 gnomAD v3.1.1 track available for hg38</h2> <p> We are happy to announce an update to the Genome Aggregation Database (gnomAD) variants track for the <a href="/cgi-bin/hgGateway?db=hg38">hg38/GRCh38</a> assembly. The <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=gnomadGenomesVariantsV3_1_1">gnomAD v3.1.1 variants</a> track contains the same underlying data as v3.1, but with minor corrections to the VEP annotations and dbSNP rsIDs. In this update, we have now included the mitochondrial chromosome data that was released as part of gnomAD v3.1 but after the UCSC version of the track was created and released. For more information about gnomAD v3.1.1, please see the related <a href="https://gnomad.broadinstitute.org/news/2021-03-gnomad-v3-1-1/" target="_blank">changelog</a>. </p> <p> We would like to thank the <a href="http://gnomad.broadinstitute.org/" target="_blank">Genome