345a74e5374d0661c43bd619450ea34372f3931f gperez2 Tue Jan 31 10:50:49 2023 -0800 Updating news and pennantIcons for the hg38 patch 14 announcement, refs #29964 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 72b0b19..b94b8b6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -42,30 +42,76 @@ <li><a href="#2006">2006 News</a></li> <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="#2001">2001</a>-<a href="#2002">2002 News</a></li> </ul> </div> </div> </div> <!-- ============= 2022 archived news ============= --> <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> +<a name="2023"></a> + +<a name="013023"></a> +<h2>Jan. 30, 2023 Addition of GRCh38 patch 14 sequences to hg38</h2> +<p> +We are pleased to announce the addition of GRCh38 patch release 14 to the +<a href="../../cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches +since its release in 2013. The GRC patch releases do not change any previously existing +sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond +to specific regions of the main chromosome sequences. For most users, the patches are unlikely +to make a difference and may complicate the analysis as they introduce more duplication.</p> + +<p> +More information on how patch sequences are incorporated can be found on the +<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +The blog post contains details about the new +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" +target="_blank">/latest</a>, +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/" +target="_blank">/initial</a>, and +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p14/" target="_blank">/p14</a> +download directories on the downloads server. With the addition of new sequences to hg38, we can +expect to see BLAT return more matches to the genome.</p> + +<ul> + <li> + The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455 + sequences, 261 alternate sequences, and no fix sequences. It is the same as the + parent download directory. This is probably the best genome file for aligners and most analysis + tasks, a version called "analysisSet" for the human genome. + </li> + <li> + The <b>p14/</b> subdirectory contains files for GRCh38.p14 (patch release 14), which has 711 + sequences, 351 alternate sequences, and 166 fix sequences. + </li> + <li> + The <b>latest/</b> symbolic link points to the subdirectory for the most recent patch version. + </li> +</ul> + +<p> +We would like to thank the <a href="https://www.ncbi.nlm.nih.gov/grc" target="_blank">Genome +Research Consortium</a> for creating the patches for hg38. We would also like to thank Galt Barber, +Jairo Navarro, and Gerardo Perez at UCSC for implementing and testing the latest patch to the +hg38 genome.</p> + <a name="2022"></a> <a name="122022"></a> <h2>Dec 20, 2022 Multiz Alignment & Conservation (470 mammals) for hg38</h2> <p> A new <a href="/cgi-bin/hgTrackUi?db=hg38&g=cons470way" target="_blank">470-way Multiz Alignment & Conservation</a> track has been added to the human <a href="/cgi-bin/hgGateway?db=hg38" target="_blank">(GRCh38/hg38)</a> genome browser. The composite track displays multiple alignments (Multiz) and measurements of evolutionary conservation (phastCons and phyloP) for 470 mammals. </p> <h3>Tracks available:</h3> <ul> <li>Multiz Alignments of 470 mammals</li> <li>470 mammals Basewise Conservation by PhyloP</li> <li>470 mammals Element Conservation by PhastCons</li>