986087931ac64c4f3ada375576fdaa6d92e7be83 abenetpa Mon May 4 16:21:41 2020 -0700 new announcement Problematic Regions track refs #24245 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 373df51..53da55e 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,68 @@ <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="050620"></a> +<h2>May 6, 2020 Problematic Regions for NGS or Sanger sequencing or very variable regions</h2> +<p> +We are happy to announce a new data track which describes +<a href="../../cgi-bin/hgTrackUi?db=hg19&g=problematic">Problematic Regions for NGS or Sanger sequencing or very variable regions</a> in the human assembly (hg19/GRCh37). +</p> + +<p> +This track shows genomic regions known to cause artefacts for common sequencing downstream analyses, +like alignment, variant, or peak calling. This track is composed of 12 subtracks with underlying +data imported from these projects: +</p> + +<ul> +<li> +<a href="../../cgi-bin/hgGateway">UCSC</a> - manually curated annotations of fixed sequences, +alternate haplotypes, unplaced contigs, pseudo-autosomal regions, and mitochondria that can yield +alignments with low quality mapping scores and discordant read pairs. </li> +<li> +<a href="https://personal.broadinstitute.org/anshul/projects/encode/rawdata/blacklists/hg19- +blacklist-README.pdf">ENCODE Blacklist</a> - comprehensive set of regions that have anomalous, +unstructured or high signal in next-generation sequencing experiments.</li> +<li> +<a href="https://www.ncbi.nlm.nih.gov/variation/tools/get-rm/">NCBI GeT-RM</a> - highly homologous +gene and exon level regions that are difficult or impossible to analyze with standard Sanger or NGS +approaches and are relevant to current clinical testing.</li> +<li> +<a href="https://www.nist.gov/programs-projects/genome-bottle">Genome-in-a-Bottle</a> - defined +regions where it is difficult to make a confident call, due to low coverage, systematic sequencing +errors, local alignment problems, etc.</li> +</ul> +</p> + +<p> +We would like to thank Anna Benet-Pages, Max Haeussler, Angie Hinrichs, and Daniel Schmelter at the +UCSC Genome Browser for planning, building, and testing these tracks. +</p> + <a name="050420"></a> <h2>May 4, 2020 May 4th data release for SARS-CoV-2 genome browser</h2> <p> We are pleased to announce our second data release for the <a target="_blank" href="/cgi-bin/hgTracks?db=wuhCor1">coronavirus genome browser</a>. Much like our <a href="#040320">first release</a>, this includes a variety of annotation types such as CRISPR tracks, protein structure and interaction tracks, immunology tracks, and a 119-way multiple sequence alignment.</p> <p> One new track we would like to highlight is the <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=publicAnnots">Crowd-Sourced Data</a> track. This track displays annotations made via a public spreadsheet available at <a target="_blank" href="http://bit.ly/cov2annots">http://bit.ly/cov2annots</a>. Any user can freely contribute to the spreadsheet, after which the annotations will display in the public coronavirus genome browser.</a>