131c2f5bfb31233b87664c985eb361dd1b0005a2 max Wed Sep 8 05:56:35 2021 -0700 making looking for a genome assembly link stand out more using CSS, refs #26081 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index 25ee5d1..b18cf61 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -2,39 +2,39 @@ <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#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="#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="#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="#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> -<li><a href="#release13">Looking for a genome assembly?</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> <a name="release1"></a> <h2>List of UCSC genome releases</h2> <h6>How do UCSC's release numbers correspond to those of other organizations, such as NCBI?</h6> <p> The first release of an assembly is given a name using the first three characters of the organism's genus and species classification in the format gggSss#, with subsequent assemblies incrementing the number. Assemblies predating the 2003 introduction of the six-letter naming system were given two-letter names in a similar gs# format and human assemblies are named hg# for human genome.</p> <table border=1> @@ -375,30 +375,75 @@ 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>. 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. +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> + +<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 +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 +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 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> In addition to the assembly versions currently available in the Genome Browser, you can access the @@ -467,60 +512,16 @@ Rest assured that work will continue. There will be updates to the assembly over the next several years. This has been the case for all other finished (i.e. essentially complete) genome assemblies as gaps are closed. For example, the <em>C. elegans</em> genome has been "finished" for several years, but small bits of sequence are still being added and corrections are being made. NCBI will continue to coordinate the human genome assemblies in collaboration with the individual chromosome coordinators, and UCSC will continue to QC the assembly in conjunction with NCBI (and, to a lesser extent, Ensembl). UCSC, NCBI, Ensembl, and others will display the new releases on their sites as they become available.</p> <a name="release11"></a> <h2>Mouse strain used for mouse genome sequence</h2> <h6>What strain of mouse was used for the Mus musculus genome?</h6> <p> C57BL/6J.</p> -<a name="release13"></a> -<h2>Looking for a genome assembly?</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 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. -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>.</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 -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 -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>. - <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->