9c30fc6ee3f85ffd90c4133518efb20198b501eb jnavarr5 Fri Jul 12 16:53:45 2024 -0700 Announcing the update to knownGene for hg19 scheduled for July 31, refs #32302 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 7b3c37a..2ea15cf 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,65 @@ </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="071224"></a> +<h2>July 12, 2024 First update to hg19's UCSC Genes track since 2013</h2> +<p> +The UCSC Genome Browser is getting ready to update hg19's UCSC Genes dataset for the first time +since 2013. In this update, the UCSC Genes track will now use GENCODE v45 gene models lifted to hg19 +and replace the old UCSC transcript IDs with the official GENCODE IDs. The anticipated released +date for this update is July 31, 2024.</p> + +<p> +As an example of what to expect, here are some GENCODE IDs that will replace the UCSC IDs in the +update:</p> + +<pre> +oldId newId +uc003qfo.3 ENST00000341911.10_8 +uc003jsk.2 ENST00000462279.5_3 +uc003umk.1 ENST00000318238.9_6 +uc003gzi.3 ENST00000682860.1_2 +uc011dpu.2 ENST00000375023.3_6 +uc021raj.2 ENST00000258149.11_6 +uc002fxp.3 ENST00000341657.9_12 +uc010xhp.1 ENST00000429344.7_6 +uc003zze.3 ENST00000242285.11_9</pre> + +<p> +For each transcript ID, the _# portion is part of the official hg19 backmap ID, so they are not +confused with the gene/transcript they are derived from in hg38. Between hg38 and hg19, the two IDs +are not always in the same sequence and may not be a one-to-one mapping. +</p> +<p> +With this update, we will also be freezing the previous 2013 knownGene release in a separate +archive track. Once new GENCODE versions are available, the previous track will then be added to the +archive for future reproducibility. More information about the knownGene archive will be available +once the update is released.</p> + <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>