db0069c4d3afe0e0834345b4665f62995cee8115 dschmelt Thu Oct 24 14:46:54 2019 -0700 Adding newsArch for Hic/Plat tracks #24273 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9ee8318..73fd0d5 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,65 @@ </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="102419"></a> +<h2>Oct. 24, 2019 Hi-C heatmap visualizations; Platinum VCFs</h2> +<h3>New Hi-C heatmap tracks and Visualization Type</h3> +<p> +We are pleased to announce a new heatmap visualization type to the UCSC Genome Browser. +These customizable heatmaps support Hi-C and other interaction based sequencing methods. +They can be configured as square, triangular, or arc interactions. You can see examples of Hi-C +regulation tracks on hg19 or hg38 assemblies.</p> +<ul> +<li> +<a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&knownGene=pack&rao2014Hic=full" target="_blank">Hi-C Heatmap Track on hg19</a></li> +<li> +<a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack&hicAndMicroC=full" target="_blank">Hi-C Heatmap Track on hg38</a></li></ul> +<p> +This track type is available for use with user data as a Custom Track or Track Hub, with the +<code>type=hic</code> specification. This visualization is suitable for publications to show +DNA-DNA interactions which may indicate TADs and loop enhancer-promoter interations. +</p> +<p class="text-center"> + <img class='text-center' src="../images/hicExample.png" width='600' alt="Example of a Hi-C Track"> +</p> + +<h3>New Platinum Genomes VCF Track</h3> +<p> +We are further pleased to announce the new Platinum Genomes VCF Tracks. These variant tracks +offer deeply seqeuenced and validated VCFs on both hg19 and hg38. This data was derived from +consensus analysis of a 17-member family pedigree to reduce potential error. +You can view the tracks below:</p> +<ul> +<li> +<a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&knownGene=pack&platinumGenomes=pack" target="_blank">Platinum Genomes Track on hg19</a></li> +<li> +<a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack&platinumGenomes=pack" target="_blank">Platinum Track on hg38</a></li></ul> + + <a name="101619"></a> <h2>Oct. 16, 2019 New GENCODE Genes tracks for human (V32) and mouse (VM23)</h2> <p> We are pleased to announce the release of updated GENCODE Genes annotation tracks for both the <a href="../cgi-bin/hgTracks?db=hg38&g=knownGene" target="_blank">hg38/GRCh38</a> and <a href="../cgi-bin/hgTracks?db=mm10&g=knownGene" target="_blank">mm10/GRCm38</a> assemblies corresponding to the <a href="http://www.ensembl.info/2019/09/26/ensembl-98-has-been-released/" target="_blank"> Ensembl 98</a> release.</p> <p> The following table provides statistics for the <a href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene" target="_blank">human V32</a> and <a href="../cgi-bin/hgTrackUi?db=mm10&g=knownGene" target="_blank">mouse VM23</a> releases derived from the GTF files that contain annotations only on the main chromosomes. More information on how