9687a91909838021ee4ca314e2a29c0cccd845c8 mspeir Sat Sep 26 16:32:35 2026 -0700 commenting out the section about loading ENCODE files as CTs, refs #24610 diff --git src/hg/htdocs/FAQ/FAQregulation.html src/hg/htdocs/FAQ/FAQregulation.html index 22999c560f5..debed8a8caa 100755 --- src/hg/htdocs/FAQ/FAQregulation.html +++ src/hg/htdocs/FAQ/FAQregulation.html @@ -158,42 +158,43 @@ <li> Pick your assembly in the panel that opens, then click <strong>UCSC</strong>.</li> </ol> <p> The Browser opens with every experiment in your filtered result set loaded as a track hub, so this works just as well for one experiment as for fifty. Restrict the search before you visualize, since a broad filter can attach a very large number of tracks at once.</p> <p> ENCODE also publishes a hub for each individual experiment, which is handy if you are scripting or want to keep a link in a session. Substitute the accession into this URL:</p> <pre>https://www.encodeproject.org/experiments/ENCSR000AKO/@@hub/hub.txt</pre> <p> and load it from the <a href="../cgi-bin/hgHubConnect#unlistedHubs">My Hubs</a> tab of the Track Hubs page, or by appending it to a browser URL as <code>hgTracks?db=hg38&hubUrl=</code> followed by the hub address.</p> +<!-- <p> If you would rather place a single file yourself, note that ENCODE distributes peaks as bigBed and signal as bigWig, both of which the Browser reads directly. Copy the file URL from the portal; you do not need to download the file. Then paste one custom track line at <a href="../cgi-bin/hgCustom">Add Custom Tracks</a>:</p> <pre>track type=bigBed name="CTCF K562 peaks" bigDataUrl=https://www.encodeproject.org/files/ENCFF002CEL/@@download/ENCFF002CEL.bigBed</pre> <p> Full instructions are on the <a href="/goldenPath/help/customTrack.html">custom tracks help page</a> and the <a href="/goldenPath/help/hgTrackHubHelp.html">track hub help page</a>.</p> - +--> <a name="promoters"></a> <h2>Promoters, enhancers and other elements</h2> <h6>Which tracks show promoters?</h6> <p> It depends on what you mean by a promoter, and the tracks disagree enough that it matters.</p> <ul> <li> <strong>EPDnew Promoters</strong> has experimentally defined promoters, each with a single, precisely mapped transcription start site. Use it when you need a defined, citable promoter region and not an approximation. On hg38 there is a companion set for non-coding RNA promoters. Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=epdNew">hg19</a>, <a href="../cgi-bin/hgTrackUi?db=hg38&g=epdNew">hg38</a> and <a href="../cgi-bin/hgTrackUi?db=mm10&g=epdNew">mm10</a>.</li>