8a904ce96a5b1e136073d1b569eba4274212dfdf gperez2 Mon Feb 13 15:09:39 2023 -0800 Announcing the release of the recombination rate track for hg38, refs #30044 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index ae558ae..539c3b1 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -48,30 +48,66 @@ </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> <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> <a name="2023"></a> +<a name="021323"></a> +<h2>Feb. 13, 2023 New recombination rate tracks for hg38</h2> +<p> +We are pleased to announce the new +<a href="/cgi-bin/hgTrackUi?db=hg38&g=recombRate2" target="_blank">recombination rate</a> tracks +for the <a href="/cgi-bin/hgGateway?db=hg38" target="_blank">GRCh38/hg38</a> genome browser. This track represents +calculated rates of recombination based on the genetic maps from +<a href="https://www.decode.com/" target="_blank">deCODE</a> and +<a href="https://www.internationalgenome.org/about" target="_blank">1000 Genomes</a>. These tracks +are organized in a super track that includes three subtracks with the deCODE recombination rates +(paternal, maternal, and average) and one subtrack with the 1000 Genomes recombination rate, which +was lifted from hg19 and can be used as a drop-in replacement for the +<a href="/cgi-bin/hgTrackUi?db=hg19&g=recombRate" target="_blank">GRCh37/hg19 track</a>. Note that +the deCODE recombination rate data is newer and has a higher resolution. Also, two subtracks that +show additional details provided by deCODE: one with the raw data of all cross-overs tagged with +their proband ID and another one with around 8000 human de-novo mutation variants that are linked to +cross-over changes. +<ul> + <li>deCODE Genetics, average from paternal and maternal</li> + <li>deCODE Genetics, paternal</li> + <li>deCODE Genetics, maternal</li> + <li>Recombination events in deCODE Genetic Map</li> + <li>De-novo mutations found in deCODE samples</li> + <li>1000 Genomes, lifted from hg19</li> +</ul></p> +<p> +More information on these tracks can be found on the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=recombRate2#TRACK_HTML" target="_blank">track description page</a>. +We would like to thank deCODE genetics, the 1000 Genomes Project, and contributors for doing the +research and making their data accessible. Thanks to Po-Ru Loh at the Broad Institute for lifting +and helping import the 1000 Genomes data to hg38. We would also like to thank Maximilian Haeussler +and Gerardo Perez for their work in creating and releasing these tracks. If you have questions, +feedback, or suggestions on this new track, please contact one of our +<a href="../contacts.html" target="_blank">Genome Browser support emails</a>.</p> + + <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/"