1d818f2b16ef453c7a9021949fd77ec4acf3d8d7 dschmelt Thu Mar 4 17:52:03 2021 -0800 Announcing refSeq update refs #26428 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 49b45e3..8708a25 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,77 @@ </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> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name=030421"></a> +<h2>Mar. 4, 2021 Updated NCBI RefSeq Gene Tracks for 13 organisms</h2> +We are pleased to announce a combination of both updated and new +<a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank"> +NCBI RefSeq gene annotation</a> tracks for the +following 13 assemblies. Most notably, we have updated both human assemblies and the new +mouse assembly.</p><br> +<div class="container"> + <div class="row"> + <div class="col-sm-3"> + <ul> + <li>Human <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=hg19">(hg19)</a></li> + <li>Human <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=hg38">(hg38)</a></li> + <li>Mouse <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=mm39">(mm39)</a></li> + <li>Worm <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=ce11">(ce11)</a></li> + </ul> + </div> + <div class="col-sm-3"> + <ul> + <li>Fruitfly <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=dm6">(dm6)</a></li> + <li>Turkey <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=melGal5">(melGal5)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=oviAri4">(oviAri4)</a></li> + <li>Yeast <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=sacCer3">(sacCer3)</a></li> + </ul> + </div> + <div class="col-sm-3"> + <ul> + <li>Frog <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=xenTro9">(xenTro9)</a></li> + <li>Pig <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=susScr11">(susScr11)</a></li> + <li>Chimp <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=panTro5">(panTro5)</a></li> + <li>Green Monkey <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=chlSab2">(chlSab2)</a><li> + </ul> + </div> + <div class="col-sm-3"> + <ul> + <li>Chinese Hamster Ovary <a href="../cgi-bin/hgTrackUi?g=refSeqComposite&db=criGriChoV1">(criGriChoV1)</a></li> + </ul> + </div> + </div> +</div> + +<p> +Thanks to <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/"> +NCBI RefSeq</a> for providing these annotations. We would also like to thank Hiram Clawson +and Daniel Schmelter of the UCSC Genome Browser group for their +work in creating and releasing these tracks.</p> + <a name="030221"></a> <h2>Mar. 02, 2021 CADD Scores now available for hg19 and hg38</h2> <p> We are happy to announce the release of a new track for human assemblies, <a href="../cgi-bin/hgTrackUi?db=hg19&chr=chrX&g=caddSuper">hg19</a> and <a href="../cgi-bin/hgTrackUi?db=hg38&chr=chrX&g=caddSuper">hg38</a>. The new track shows <a href="https://cadd.gs.washington.edu/" target="_blank">Combined Annotation Dependent Depletion (CADD)</a> scores for each base in the genome and corresponds to the v1.6 developmental release. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also highly rank causal variants within individual genome sequences. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS.</p> @@ -1402,31 +1449,31 @@ <p> We are happy to share a new data set, 1000 Genomes Trios on hg38, and a visualization tool for displaying chromosome phased VCFs and family inheritance patterns. This track shows phased variants from seven trios of parents and child across different regions. You can infer which parent passed on which variant and identify possible de-Novo variants. The data was produced by <a href="https://www.internationalgenome.org/" target="_blank">International Genome Sample Resource (IGSR)</a> from sequence data generated by the <a href="https://www.internationalgenome.org/about" target="_blank">1000 Genomes Project</a>. For more information on the 1000 Genomes Trios track and the VCF Trio format, please visit the track description page and VCF help page: </p> <ul> <li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=tgpTrios"> 1000 Genomes Trios on GRCh38/hg38</a></li> -<li><a href="https://genome.ucsc.edu/goldenPath/help/vcf.html#trio">VCF track format</a></li> +<li><a href="<li><a href="../goldenPath/help/vcf.html#trio">VCF track format</a></li> </ul> <div class="text-center"> <a href="../../cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=tgpTrios"> <img width="80%" height="80%" src="../../images/trioExample.png" alt="3 VCF Phased Trio tracks along with the GENCODE v32 genes from the Human/GRCh38 assembly. Each of two diploid haplotypes for each individual in a trio is drawn as a black lane, with snps as vertical ticks on the haplotype they fall on. Ticks are shaded blue,red,green or black according to their predicted functional effect."></a> </div> <p> We would like to thank the IGSR and 1000 Genomes Project teams and contributors for doing the research and making their data accessible. We would also like to thank Chris Lee, Daniel Schmelter, and Angie Hinrichs for designing, developing, and releasing this track.</p>