8ea0ade717747f936e7bda4f09bf848fe16a1c8f dschmelt Fri Sep 24 17:18:41 2021 -0700 Updating info and readability to let users know which assemblies we have and where refs #28205 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index b18cf61..7ab18f1 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -378,71 +378,66 @@ <ul> <li>NCBI genomes are repeat masked with RepeatMasker, however, UCSC genomes are independently masked with both RepeatMasker (with different flags) and WindowMasker, ultimately using the program output with the highest percentage masked for the base sequence</li> <li>In genome download files, UCSC uses the 'chr1' nomenclature for sequence identifiers, whereas the primary NCBI sequence identifiers are RefSeq accessions</li> <li>The original mitochondrion (chrM) for hg19 differs from the one in NCBI (GRCh37)</li> <li>The mitochondrion released by NCBI after the hg19 browser was built has been added to the assemby as chrMT. See our <a href = "FAQgenes.html#mito" target = _blank>documentation</a> for details.</li> </ul> <h2 id=release13>Looking for a genome assembly not shown in the tree?</h2> <p> When looking for a specific assembly, the best place to start is the <a -href="/cgi-bin/hgGateway">Gateway page</a>. The species tree shows all genomes with -annotations added and reviewed by UCSC. If you begin to type the common species name or -NCBI accession number in the -search box on the left side of the screen, the text will autocomplete if any matches are found. +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 also <a href="/cgi-bin/hgHubConnect">Public Hubs</a>, thousands -of genomes with annotations not reviewed by UCSC but still available for browsing.</p> +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 there is no match for the assembly on the gateway page, you may search our -<a href="../goldenPath/newsarch.html#060121">GenArk</a> (Genome Archive) -<a href="https://hgdownload.soe.ucsc.edu/hubs/">archive of assembly hubs</a>. These include -a large number of NCBI assemblies, as well as Vertebrate Genomes Project assemblies. Many -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> -when the <b>GCF</b> accession is known. Note that -many of these are also Public Hubs, and will show up on a <a -href="/cgi-bin/hgGateway">Gateway page</a> search.</p> - -<p> -If the assembly of interest is not found in either location, you may write in to our mailing +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" href="https://www.ncbi.nlm.nih.gov/assembly/docs/submission/"> Assembly Submission Guidelines page</a> at NCBI for directions on their submission process.</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 +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>. +<a href="/cgi-bin/hgHubConnect">Public Hub</a>.</p> <a name="release12"></a> <h2>Differences between UCSC and NCBI mouse assemblies</h2> <h6>Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?</h6> <p> The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds.</p> <a name="release5"></a> <h2>Accessing older assembly versions</h2> <h6>I need to access an older version of a genome assembly that's no longer listed in the Genome Browser menu. What should I do?</h6> <p>