da0c649ca5158c447b4dc004cbfcc1eddac1203f dschmelt Thu Nov 14 16:45:59 2019 -0800 Fixing old crusty url, refs #24470 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2006028..8ba490d 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,50 @@ </div> <div class="col-sm-3"> <ul> <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> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> +<a name="111319"></a> +<h2>Nov. 13, 2019 Hi-C Heatmaps now supported for Custom Tracks and Track Hubs</h2> +<p> +We are happy to announce that Hi-C heatmaps can now be used to visualize +custom Hi-C data as Custom Tracks and Track Hubs. This heatmap visualization shows +interaction scores for contact sequencing methods which may indicate +enhancer-promoter interactions. Supporting users' Hi-C data is the next +step in our support for 3C sequencing data, following the +<a href="#102519b">popular Hi-C tracks</a> on +<a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&knownGene=pack&rao2014Hic=full" +target="_blank">hg19</a> and <a +href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack&hicAndMicroC=full" +target="_blank">hg38</a> as well as the +<a href=#081018>Interact format used in GeneHancer</a> for low-density +interactions.</p> + +<p> +Information and examples of displaying your own Hi-C data can be found +on the <a href="help/hic.html">hic track format help page</a>. + <a name="110519"></a> <h2>Nov. 5, 2019 Expanded CRISPR track released for mouse (GRCm38/mm10)</h2> <p> We are pleased to announce the release of an expanded <a href="../cgi-bin/hgTracks?db=mm10&hideTracks=1&knownGene=pack&crisprAllTargets=pack&position=chr1:11186551-11186838" target="_blank">CRISPR Targets track</a> for the mouse (GRCm38/mm10) assembly. This track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire mouse genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. </p> <p class="text-center"> <img class='text-center' src="../images/mm10CrisprAll.png" width='800' alt="CrisprAllTargets track"> </p> @@ -9913,31 +9933,31 @@ page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="050405"></a> <h2>May 5, 2005 New Mouse assembly available in Genome Browser</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 34 (UCSC version mm6), is now available in the UCSC Genome Browser. In conjunction with this release, we have archived mouse assemblies mm3 and mm4. All archived assemblies are available for download via our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse" target="_blank">downloads server</a>.</p> <p> The Build 34 assembly has an assembled length of approximately 2.6 Gb, of which about 1.9 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI -<a href="www.ncbi.nlm.nih.gov/genome/guide/mouse/release_notes.html" +<a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/release_notes.html" target="_blank">Build 34 Data</a> web page. NOTE: In the Genome Browser mm6 assembly, chrY_random erroneously contains a region duplicated from chrY. For more information about this issue, see the Genome Browser <a href="../FAQ/FAQdownloads.html#download30">FAQ</a>. Please also note that the UCSC mm6 database contains only the reference strain C57BL/6J.</p> <p> The mm6 sequence and annotation data may be downloaded from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm6/">FTP server</a> or <a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm6/">Downloads</a> web page. The mm6 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Mirror sites, please note: due to the size of the comparative genomics annotations in this assembly, the data set requires an unusually large amount of disk space. If you regularly download updates of the mouse data to your site, you may want to examine your available disk space before adding the annotation database from this assembly and/or reschedule your download for a period of low activity on your server. The size of the mm6 annotation database directory