483ee22a127c4f2fc29aca3752227232df09f2ab brianlee Fri Apr 22 09:21:31 2022 -0700 Adding a note about the new assemblyRequest.html page on the FAQ about genomes refs #29237 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index 8fed8f5..93e2e11 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -394,41 +394,41 @@ href="/cgi-bin/hgGateway">Gateway page</a>. If you begin to type the common name, species name, or NCBI RefSeq accession number in the search box on the left side of the screen, suggestions will appear if any matches are found. This search will also match any <a href="/goldenPath/help/hgTrackHubHelp.html#Assembly"> assembly hubs</a> that are listed in UCSC's <a href="/cgi-bin/hgHubConnect">Public Hubs</a>. Nearly every NCBI RefSeq assembly and Vertebrate Genomes Project assembly is included here within the <a href="../goldenPath/newsarch.html#060121">GenArk hubs</a>. NCBI RefSeq assemblies can be loaded with direct links such as <a href="http://genome.ucsc.edu/h/GCF_001984765.1"> http://genome.ucsc.edu/h/GCF_001984765.1</a> with the <b>GCF</b> accession. These assembly hubs are automatically updated, but not reviewed by UCSC. The species tree shows all genomes reviewed by UCSC.</p> <p> -If the assembly of interest is not found, you may write in to our mailing -list -(<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>) -including the <a target="_blank" -href="https://www.ncbi.nlm.nih.gov/assembly">NCBI Genbank assembly accession</a> for the requested -assembly in the message. These will start -with either <b>GCA_</b> or <b>GCF_</b>. Our agreement with the genomics community is -that we wait until the assembly has been deposited -into Genbank at NCBI before we process it. See the <a target="_blank" +If the assembly of interest is not found, please visit our +<a href="/assemblyRequest.html">assembly request page</a>. +Search that page for your assembly, if there is a "view" +link you can launch the existing genome browser. Otherwise, +click the "request" button to fill out a form to +add your genome of interest. An existing <b>GCA_</b> or <b>GCF_</b> +identifier must exist, reflecting the assembly has been deposited +into Genbank at NCBI before we can process it. See the <a target="_blank" href="https://www.ncbi.nlm.nih.gov/assembly/docs/submission/"> -Assembly Submission Guidelines page</a> at NCBI for directions on their submission process. +Assembly Submission Guidelines page</a> at NCBI for directions on +their submission process if your genome needs to be deposited. Also, review the <a target="_blank" href="https://bit.ly/UCSC_blog_GenArk"</a>UCSC GenArk Blog posts</a> for examples of accessing and reviewing technical details about GenArk hubs.</p> <p> Another option available to all users is to create an <a href="/goldenPath/help/hgTrackHubHelp.html#Assembly"> assembly hub</a>. These are assemblies created and hosted by users and displayed on the Genome Browser. This requires no intervention by the UCSC Genome Browser and can be done for any assembly. See our <a href="/goldenPath/help/hubQuickStartAssembly.html"> Quick Start Guide to Assembly Hubs page</a> for additional information and resources. If you create an assembly hub, consider sharing it with others as a <a href="/cgi-bin/hgHubConnect">Public Hub</a>.</p> <a name="release12"></a> <h2>Differences between UCSC and NCBI mouse assemblies</h2>