791fedf2a50003798bff046bd22f01bb16af3ea0 dschmelt Thu Aug 6 17:56:23 2020 -0700 Draft annoucement for Covid track release refs #25984 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9e9f300..4ddc642 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,66 @@ <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="080720"></a> +<h2>Aug. 07 2020 Eight new data tracks for SARS-CoV-2 (COVID) </h2> +<p> +We are working hard to support the scientific effort against the COVID pandemic and are happy +to announce eight new data track annotations for the SARS-CoV-2 genome. +Like nearly all of our tracks, the data are open-access +and downloadable through our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#SARS-CoV-2"> +Downloads page</a> or <a href="../../cgi-bin/hgTables">Table Browser</a> page. +More information on each of these datasets can be obtained by reading the data +track descriptions linked below.</p> +<ul> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=problematicSites">Problematic sites</a> shows +regions that are ambiguous and may warrant caution or masking for analysis.</li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=rapid">RAPID Primers</a> +marks regions that were successfully used for Nanopore sequencing. </li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=unipCov2AliSwissprot">Updated UniProt proteins</a> +which displays UniProt protein sequences mapped to the SARS-CoV-2 genome</li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=phyloGenes">PhyloCSF Genes</a> +showing curated SARS-CoV-2 protein-coding genes conserved within the Sarbecovirus subgenus +as calculated with comparative genomics algorithms.</li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=addgene">AddGene Plasmid Alignments</a> + describing sequences contained in Addgene plasmids that align to the SARS-CoV-2 genomes.</li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=contacts">Protein Db Ligand Contact residues</a> +showing potential contact amino acids for ligands, inferred from structures in the Protein +Database (PDB).</li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=nextstrainParsimony">Nextstrain Parsimony Scores</a> +showing scores of how variants are distributed in a phylogenetic tree.</li> +<li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=nextstrainFreq">Nextstrain variants frequency</a> +showing occurrence counts of each SARS-CoV-2 variant in GSAID sequences.</li> +</ul> +<p> +We would like to acknowledge the work of the UCSC Genome Browser team and the data collaborators. +Thank you to the research community for creating, sharing, and using this important +data to propel science in light of this pandemic.</p> + + <a name="080320"></a> <h2>Aug. 3, 2020 Annotated SNVs track for Rhesus Macaque (rheMac10)</h2> <p> We are pleased to announce an annotated SNVs track for the Rhesus macaque (rheMac10) assembly. SNVs were called using the Genome Analysis Toolkit (GATK), then the Variant Effect Predictor software was used to predict the functional consequence of SNVs. Ensembl release 98 gene models were used in the predictions, which are based on both Ensembl and RefSeq gene predictions as well as PacBio iso-seq data.</p> <p> For more information including a credits and methods section, see the <a target="_blank" href="/cgi-bin/hgTrackUi?db=rheMac10&g=rhesusSNVs">track description page</a>.</p> <p> We would like to thank the Rhesus Macaque Genome Consortium and <a target="_blank" href="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project"> Jeff Rogers' lab at BCM-HGSC</a> for supplying the data for this track. We would