9add99453760c10170441f9ac73add6f17126b62 lrnassar Tue Jan 11 17:03:51 2022 -0800 Officially archiving the 2021 news, and adding new 2022 tag. No RM diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index dd7dac5..a89dd1f 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -37,32 +37,34 @@ <li><a href="#2007">2007 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2006">2006 News</a></li> <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="#2001">2001</a>-<a href="#2002">2002 News</a></li> </ul> </div> </div> </div> -<!-- ============= 2021 archived news ============= --> -<a name="2021"></a> +<!-- ============= 2022 archived news ============= --> +<a name="2022"></a> + + <a name="010622"></a> <h2>Jan. 6, 2022 JASPAR Transcription Factor Binding Site track available for human and mouse</h2> <p> We are happy to announce the new JASPAR 2022 track for human (<a href="/cgi-bin/hgTrackUi?db=hg19&g=jaspar">GRCh37/hg19</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=jaspar">GRCh38/hg38</a>) and mouse (<a href="/cgi-bin/hgTrackUi?db=mm39&g=jaspar">GRCm39/mm39</a> and <a href="/cgi-bin/hgTrackUi?db=mm10&g=jaspar">GRCm38/mm10</a>). With this release, we are also introducing the JASPAR 2020 track for GRCm38/mm10. </p> <p> These tracks represent genome-wide predicted binding sites for transcription factor binding profiles in the <a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR CORE collection</a>. JASPAR CORE is an open-source database containing a curated, non-redundant set of binding profiles @@ -75,30 +77,33 @@ Binding site predictions and UCSC tracks were computed by the <a href="http://cisreg.ca/" target="_blank">Wasserman Lab</a>. We would like to thank Daniel Schmelter and Jairo Navarro at UCSC for building and testing these tracks.</p> <a name="122021"></a> <h2>Dec. 20, 2021 Last of three blog posts about new GenArk hubs</h2> <p> We are pleased to announce the third blog post in a three-part series about our new GenArk Assembly Hubs. This <a href="https://genome-blog.soe.ucsc.edu/blog/2021/12/20/genark-hubs-part-3/" target="_blank">final installment</a> provides some explanation of the technical details behind the process. The <a href="https://bit.ly/UCSC_blog_GenArk1">first post</a> was about accessing the data, and the <a href="https://bit.ly/UCSC_blog_GenArk2">second post</a> shared examples of using the hub's data with BLAT, PCR, and External Tools.</p> +<!-- ============= 2021 archived news ============= --> +<a name="2021"></a> + <a name="121621"></a> <h2>Dec. 16, 2021 Track Hub Filters Quick Start Guide</h2> <p> We are pleased to announce a help page specific to building filters on Track Hubs. <a href="help/hgTrackHubHelp.html#Intro">Track Hubs</a> are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser. Track Hubs allow a lab to share and host all their genomic data (<a href="help/bam.html">BAMs</a>, <a href="help/vcf.html">VCFs</a>, ect.) via a single Genome Browser link. Such links can load multiple hubs and even be combined with a position parameter to easily reference laboratory data around a gene of interest, see examples in a recent <a href="https://bit.ly/UCSC_blog_sharing">blog bost</a> about sharing data with URLs.</p> <p> The <a href="help/hubQuickStartFilter.html">Track Hub Filters Quick Start Guide</a> provides example hubs employing new extensive <a href="help/trackDb/trackDbHub.html#filter">filter</a> settings available for Track Hubs.</p> <p> @@ -4600,30 +4605,31 @@ (<a href="https://academic.oup.com/gigascience/article/6/7/gix038/3836916" target="_blank">Zheng-Bradley et al.</a>). Variant discovery and quality control were performed as described in (<a href="https://wellcomeopenresearch.org/articles/4-50" target="_blank">Lowy-Gallego et al.</a>).</p> <p> Variants were called on the autosomes (chromosomes 1 through 22) and on the Pseudo-Autosomal Regions (PARs) of chromosome X. Therefore this track has no annotations on alternate haplotype sequences, fix patches, chromosome Y, or the non-PAR portion (the majority) of chromosome X.</p> <p> We would like to thank the IGSR for making these variant calls freely available. We would also like to thank Angie Hinrichs and Jairo Navarro for their efforts in creating and reviewing this track. </p> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> + <a name="121319"></a> <h2>Dec. 13, 2019 New dbSNP pipeline: dbSNP b153 release, bigDbSnp track type</h2> <p> We are pleased to announce a new dbSNP pipeline, along with the first new dataset: dbSNP b153 for <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=dbSnp153Composite">hg19</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&g=dbSnp153Composite">hg38</a>.</p> <p> dbSNP has seen an <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/02/dbsnp-database-doubles-size-twice-13-months/"> explosive growth</a> in recent releases, from roughly 324 million variants in <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/dbsnps-human-build-150-has-doubled-the-amount-of-refsnp-records/"> build 150</a>, to over 700 million variants in the latest build b153. In an effort to continue providing efficient access to these data, dbSNP has redesigned their <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/07/07/dbsnp-redesign-supports-future-data-expansion/"> architecture and data flow</a>. We have also taken this opportunity to redesign our dbSNP