fa272dac584b8d450211f426b50c5e9e6de114c8 mspeir Tue Sep 22 08:40:34 2026 -0700 New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/FAQ/index.html src/hg/htdocs/FAQ/index.html index 26b8dd2bfb9..71504d53f73 100755 --- src/hg/htdocs/FAQ/index.html +++ src/hg/htdocs/FAQ/index.html @@ -1,117 +1,118 @@ <!DOCTYPE html> <!--#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>Genome Browser FAQ</h1> <p> This page contains responses to frequently asked questions from our user community. A full list of public questions is available for search from our <a href="https://groups.google.com/a/soe.ucsc.edu/group/genome?hl=en" target="_blank">Genome Browser mailing list</a>. To ask a question, please visit our <a href="../contacts.html">Contact Us</em></a> page.</p> <h2>FAQ categories</h2> <div class="row"> <div class="col-md-5"> <ul> <li><a href="FAQformat.html">Data File Formats</a></li> <li><a href="FAQblat.html">Blat sequence alignment</a></li> <li><a href="FAQdownloads.html">Data and Downloads</a></li> <li><a href="FAQgenes.html">Genes and Gene Tracks</a></li> <li><a href="FAQreleases.html">Assembly Releases and Versions</a></li> <li><a href="FAQtracks.html">Genome Browser Tracks</a></li> +<li><a href="FAQregulation.html">Regulation and cis-regulatory tracks</a></li> <li><a href="FAQlink.html">Linking to the Genome Browser</a></li> <li><a href="FAQcustom.html">Custom Annotation Tracks</a></li> <li><a href="FAQcite.html">Citing the Genome Browser</a></li> <li><a href="FAQlicense.html">Mirroring or Licensing the Genome Browser</a></li> <li><a href="FAQdisplay.html">Display Problems</a></li> <li><a href="../ENCODE/FAQ/index.html">ENCODE Resources and FAQ</a></li> <li><a href="FAQmaillist.html">Posting a question to the mailing list</a></li> </ul> </div> <div class="col-md-7"> <!-- Search GB FAQ --> <form name="googleForm0" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm0.q.value=document.googleForm0.qq.value+' site:genome.ucsc.edu/FAQ/';"> <p> Search the Genome Browser FAQs: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=25 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <!-- Search GB help documentation --> <form name="googleForm2" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm2.q.value=document.googleForm2.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> <p> Search the Genome Browser help pages: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=25 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <!-- Search entire GB site --> <form name="googleForm1" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/';"> <p> Search the entire Genome Browser website: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=25 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <!-- Search Wiki pages --> <form name="googleForm3" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm3.q.value=document.googleForm3.qq.value+' site:genomewiki.ucsc.edu/';"> <p> Search our user-edited wiki website: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=25 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <!-- Search GB genomic data (gateway page) --> <p> Search for genomic data from our <a href="../cgi-bin/hgGateway" target="_blank">organism Gateway page</a>, <a href="../cgi-bin/hgTracks?hgt_tSearch=track+search" target="_blank"> Track search page</a>, or <a href="../cgi-bin/hgHubConnect#publicHubs" target="_blank"> Public Hub</a> collection.</p> <!-- Search mailing list archives --> <p> Search our main mailing list archives for previous answers about <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">website and data questions</a>, or our secondary mailing list for <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror" target="_blank">mirror and source code questions</a>, or our previous <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce" target="_blank">Genome Browser announcements</a> about new software and data releases.</p> </div> </div> <hr> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->