e17e7664c435f802e6c78ac140593f5f817419a5 brianlee Wed May 25 09:27:01 2022 -0700 News about assembly request page, hint to show all beyond 1st 500 on page refs #29237 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d5d646a..4a91bda 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -64,31 +64,33 @@ </a> </div> <p>Our most recent blog post, <a href="https://genome-blog.soe.ucsc.edu/blog/2022/04/12/genark-hubs-part-4/" target="_blank">GenArk Hubs Part 4 - New assembly request page</a> describes how to use this new feature.</p> <p> With the realization that we could not possibly host every single genomic assembly available, we created <a href="help/hgTrackHubHelp.html#Assembly">Assembly Hubs</a>. Assembly Hubs allow anyone to host and view the genome of any species in the context of the UCSC Genome Browser. Last summer we <a href="newsarch.html#060121">announced</a> the creation of the Genome Archive (GenArk) which included Assembly Hubs for the genomic assemblies of more than 1,300 species. Since then, we have taken this a step further by creating this new <a href="/assemblyRequest.html" target="_blank">Assembly Request</a> page that displays about 14,000 assemblies: those that are available for viewing and those that can be requested. We currently have nearly 1,700 assembly -hubs available for viewing at the click of a button. If you don't see the organism or assembly you +hubs available for viewing at the click of a button. Upon first visiting the page shows only +<b>the first 500 assemblies</b>. Use the <em>select assembly type to display</em> button to +"show all" assemblies. If you don't see the organism or assembly you are interested in then please use the page to request it. We will build an Assembly Hub for you and let you know when it is available for viewing.</p> <a name="051122"></a> <h2>May 11, 2022 New GENCODE gene tracks: Human V40 (hg19/hg38) - Mouse M29 (mm39)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="https://www.ensembl.info/2022/04/12/ensembl-106-has-been-released/" target="_blank">Ensembl 106</a>, for three assemblies: <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV40lift37">hg19/GRCh37</a>, <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=wgEncodeGencodeV40">hg38/GRCh38</a>, and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM29">mm39/GRCm39</a>. For human, the GENCODE V40 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