ab9e4c7bf0b20c84cae8c0c144e97ac5046f8313 gperez2 Wed Jan 8 08:37:26 2025 -0800 Updated the FAQreleases.html#release13 entry and added a link to assemblySearch.html, refs #32596 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index 9c2b67a..7ebf837 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -3,31 +3,31 @@ <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Assembly Releases and Versions</h1> <h2>Topics</h2> <ul> <li><a href="#release1">List of UCSC genome releases</a></li> <li><a href="#release2">Initial assembly release dates</a></li> <li><a href="#patches">Patch sequences for human and mouse</a></li> <li><a href="#release3">UCSC assemblies</a></li> <li><a href="#release4">Comparison of UCSC and NCBI human assemblies</a></li> -<li><a href="#release13">Looking for a genome assembly not shown in the tree?</a></li> +<li><a href="#release13">Finding a genome assembly</a></li> <li><a href="#release12">Differences between UCSC and NCBI mouse assemblies</a></li> <li><a href="#release5">Accessing older assembly versions</a></li> <li><a href="#release6">Frequency of GenBank data updates</a></li> <li><a href="#release7">Coordinate changes between assemblies</a></li> <li><a href="#release8">Converting positions between assembly versions</a></li> <li><a href="#snpConversion">Converting SNPs between assembly versions</a></li> <ul> <li><a href="#snpConversion">How can I convert SNP annotation coordinates between assembly versions?</a></li> <li><a href="#snpLarge">How can I convert a large set of SNP annotations?</a></li> <li><a href="#snpExtract">How can I extract a list of rsIDs using chrom:start-end or vise versa?</a></li> </ul> <li><a href="#release9">Missing annotation tracks</a></li> <li><a href="#release10">What next with the human genome?</a></li> <li><a href="#release11">Mouse strain used for mouse genome sequence</a></li> </ul> @@ -423,75 +423,51 @@ Human assemblies displayed in the Genome Browser (hg10 and higher) are near identical to the NCBI assemblies when it comes to primary sequence. Minor differences may be present, however. Sources include:</p> <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>. 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> - +<h2 id=release13>Finding a genome assembly</h2> <p> -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 that 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 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> - +If the assembly of interest is not listed on the <a href="/cgi-bin/hgGateway">Gateway page</a>, +visit the <a href="/assemblySearch.html">Genome assembly search and request page</a>. Search for the +assembly, and if no "view" link exists, click "request" to submit a form. A +GCA_ or GCF_ identifier is required, indicating the assembly is deposited in GenBank at NCBI. For +additional details, refer to +<a target="_blank" href="https://www.ncbi.nlm.nih.gov/assembly/docs/submission/"> +NCBI's Assembly Submission Guidelines</a> and the +<a target="_blank" href="https://bit.ly/UCSC_blog_GenArk"</a>UCSC GenArk Blog</a>.</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> - -<p> -If you would like information about creating a track hub for an existing assembly hub, please refer -to the following <a href="/FAQ/FAQlink.html#trackHubLoading">FAQ entry</a>.</p> +<a href="/cgi-bin/hgHubConnect">Public Hub</a>. If you would like information about creating a +track hub for an existing assembly hub, please refer to the following +<a href="/FAQ/FAQlink.html#trackHubLoading">FAQ entry</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>