b17dc39da7b8b002eabc409c792c022038e8e126 brianlee Mon Jun 6 10:36:33 2022 -0700 Changes for code review, refs #29524 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index a10db8e..7c2eb5e 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -79,32 +79,32 @@ <h2>May 24, 2022 New Assembly Request Page</h2> <p> Find the genome of your favorite organism on our new <a href="/assemblyRequest.html" target="_blank">assembly request</a> page. Click "view" to launch a browser, or the "request" button to request that we add yours.</p> <div class="text-center"> <a href="/assemblyRequest.html"> <img src="../images/newsArchImages/requestPage.png" alt="New Assembly Request Page" width="700"> </a> </div> <p>Our most recent blog post, <a href="https://genome-blog.soe.ucsc.edu/blog/2022/04/12/genark-hubs-part-4/" target="_blank">GenArk Hubs Part 4 - New assembly request page</a> describes how to use this new feature.</p> <p> -With the realization that we could not possibly host every single genomic assembly available, -we created <a href="help/hgTrackHubHelp.html#Assembly">Assembly Hubs</a>. Assembly Hubs allow +With the realization that we could not possibly host every single genomic assembly available,we created +<a href="help/hgTrackHubHelp.html#Assembly" target="_blank">Assembly Hubs</a>. Assembly Hubs allow anyone to host and view the genome of any species in the context of the UCSC Genome Browser. Last summer we <a href="newsarch.html#060121">announced</a> the creation of the Genome Archive (GenArk) which included Assembly Hubs for the genomic assemblies of more than 1,300 species. Since then, we have taken this a step further by creating this new <a href="/assemblyRequest.html" target="_blank">Assembly Request</a> page that displays about 14,000 assemblies: those that are available for viewing and those that can be requested. We currently have nearly 1,700 assembly hubs available for viewing at the click of a button. Upon first visiting the page shows only <b>the first 500 assemblies</b>. Use the <em>select assembly type to display</em> button to "show all" assemblies. If you don't see the organism or assembly you are interested in then please use the page to request it. We will build an Assembly Hub for you and let you know when it is available for viewing.</p> <a name="051122"></a> <h2>May 11, 2022 New GENCODE gene tracks: Human V40 (hg19/hg38) - Mouse M29 (mm39)</h2> @@ -292,31 +292,31 @@ <p> We are happy to announce the release of the ReMap Atlas of Regulatory Regions track for <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=ReMap">hg38</a>, <a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=ReMap">hg19</a>, <a href="/cgi-bin/hgTrackUi?db=mm39&c=chrX&g=ReMap">mm39</a>, <a href="/cgi-bin/hgTrackUi?db=mm10&c=chrX&g=ReMap">mm10</a>, and <a href="/cgi-bin/hgTrackUi?db=dm6&c=chr4&g=ReMap">dm6</a>. These tracks represent the <a href="https://remap.univ-amu.fr/" target="_blank">ReMap Atlas</a> of regulatory regions, which consists of a large-scale integrative analysis of all Public ChIP-seq data for transcriptional regulators from GEO, ArrayExpress, and ENCODE. Each transcription factor follows a specific RGB color. Individual BED files for specific TFs, cells/biotypes, or data sets can be found and downloaded on the <a href="https://remap.univ-amu.fr/download_page" target="_blank">ReMap website</a>. </p> <p> -The below image shows the ReMap ChIP-seq Track, where a right-click can bring up the configuration +The image below shows the ReMap ChIP-seq Track, where a right-click can bring up the configuration option. Then there are filters available using either regular expression (regexp) or wildcards. In the image <code>.*A\|B\|F.*</code> is using regexp, which will select all Transcriptional regulators that include either the letter A, B, or F, while a separate wildcard filter on the Biotypes field, <code>MC*</code>, selects all tissue names starting with MC. Drop-down menus also exist to perform the same filters, as well as the ability to customize the label, for instance, to only show the Biotype.</p> <div class="text-center"> <img src="../images/newsArchImages/ReMap.png" alt="ReMap Filter" width="1000"> </div> <p> We would like to thank Benoit Ballester and the ReMap team at <a href="https://tagc.univ-amu.fr/" target="_blank">TAGC INSERM</a> (Inserm National Institute of Health and Medical Research) for making this data available. We also want to thank Max Haeussler, Gerardo Perez and Jairo Navarro for the creation and release of these tracks. </p>