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
@@ -13,30 +13,31 @@
 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/';">