9c2dfa33b42a7ff3d3e21b70872d6fe3b7a62d0b lrnassar Tue May 5 10:27:24 2020 -0700 Undoing and recomitting Ana's announcement - she accidentally changed the formatting on newsarchive page, no RM diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 53da55e..f7f768b 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -44,58 +44,55 @@ <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> +<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> +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>