d052043384f869056aa55296e967077b9afb5970 lrnassar Thu Jun 18 16:58:38 2020 -0700 Releasing updated chain self tracks refs #24695 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 595987b..346d620 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,49 @@ </div> <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> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> + +<a name="061920"></a> +<h2>Jun. 19, 2020 Updated Self Chain track for human (GRCh38/hg38)</h2> +<p> +We have updated the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr16&g=chainSelf"> +Self Chain</a> track for the human GRCh38/hg38 assembly. The Self Chain track shows +alignments of the human genome with itself, using a gap scoring system that allows longer +gaps than traditional affine gap scoring systems. After filtering out the alignments produced +when identical locations of the genome map to one another (e.g. chrN mapping to chrN), the +remaining alignments point out areas of duplication within the human genome.</p> +<p> +The updated +track now includes 33,039,051 chains, and should provide improved sensitivity for pseudogenes +and other homologous regions. For more information, see the track <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&c=chr16&g=chainSelf">description page</a>.</p> +<p> +We would like to thank Angie Hinrichs, Anna Benet-Pages, and Lou Nassar for the development +and release of this track.</p> + <a name="061820"></a> <h2>Jun. 18, 2020 New ENCODE cCREs track available for human and mouse (hg38 and mm10) </h2> <p> We are pleased to announce the <em>ENCODE Registry of candidate cis-Regulatory Elements</em> (cCREs) track for the human and mouse genomes (<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=encodeCcreCombined" target="_blank">GRCh37/hg19</a> and <a href="../../cgi-bin/hgTrackUi?db=mm10&c=chrX&g=encodeCcreCombined" target="_blank">GRCm38/mm10</a>). cCREs are the subset of representative DNase hypersensitive sites across ENCODE and Roadmap Epigenomics samples that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. The Registry of cCREs is one of the core components of the integrative level of the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Encyclopedia of DNA Elements</a>. A total of 926,535 elements for human and 339,815 elements for mouse were identified @@ -651,31 +670,31 @@ href="https://gnomad.broadinstitute.org/faq">gnomAD</a> site. </p> <p class="text-center"> <img class='text-center' src="../images/GnomadConstraintStructruralVarRelease.PNG" width='80%' alt="Example of Constraint Metrics and Structural Variants tracks"> </p> <p> We would like to thank the <a target="_blank" href="https://gnomad.broadinstitute.org">Genome Aggregation Database Consortium</a> for making these data available. We would also like to thank Christopher Lee, Maximilian Haeussler, Lou Nassar, Jairo Navarro, Robert Kuhn and Anna Benet-Pages for their effort in the creation of these tracks. </p> -<a name="042020"></a +<a name="042020"></a> <h2>Apr. 20, 2020 New video on the Browser's YouTube channel</h2> <p> We have released a new video to the Browser's <a href = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target = _blank>YouTube channel</a>. </p> <p> <b> Browser Basics, Part Two — Configuring the Browser </b> </p> <p> This <a href = "https://bit.ly/ucscVid18" target = _blank>video</a>