3814d8eec23ed1c9f539f669383099eb605dbbcd mspeir Sat Sep 26 18:18:00 2026 -0700 Regulation FAQ: link hgCustom as well as the custom track help, refs #24610 diff --git src/hg/htdocs/FAQ/FAQregulation.html src/hg/htdocs/FAQ/FAQregulation.html index debed8a8caa..8e06956e0c6 100755 --- src/hg/htdocs/FAQ/FAQregulation.html +++ src/hg/htdocs/FAQ/FAQregulation.html @@ -120,33 +120,34 @@ experiments that were available when it was built, so if your factor is absent from ReMap there may be no public ChIP-seq for it in that organism. The <a href="https://remap.univ-amu.fr/" target="_blank">ReMap website</a> lets you search by target and download the peaks per factor, and that is the quickest way to check.</p> <p> If the experiment exists but is newer than our tracks, or was done in a cell type we do not carry, you will need to load the data yourself as a custom track. The usual sources are:</p> <ul> <li> The <a href="https://www.encodeproject.org/" target="_blank">ENCODE portal</a>, for anything produced by ENCODE. This is the easiest case, because the portal will send the data straight to our browser for you. See the <a href="#encodePortal">next question</a>.</li> <li> <a href="https://www.ncbi.nlm.nih.gov/geo/" target="_blank">GEO</a>, for data submitted alongside a publication. Many GEO submissions include processed peak files as supplementary - material, usually BED or narrowPeak, which you can load as a - <a href="/goldenPath/help/customTrack.html">custom track</a> after checking that the - coordinates match the assembly you are using.</li> + material, usually BED or narrowPeak, which you can + <a href="/goldenPath/help/customTrack.html">load as a custom track</a> at + <a href="../cgi-bin/hgCustom">Add Custom Tracks</a>, after checking that the coordinates + match the assembly you are using.</li> <li> <a href="https://www.ncbi.nlm.nih.gov/sra" target="_blank">SRA</a>, for raw sequencing reads. The Browser cannot display SRA data. Raw reads have to be aligned and peak-called before there is anything to show, which is a job for a sequence analysis pipeline rather than for us.</li> </ul> <a name="encodePortal"></a> <h6>How do I display ENCODE data that is not already a track?</h6> <p> You do not need to download anything or write a custom track by hand. The ENCODE portal will open its data in the Genome Browser for you.</p> <ol> <li> Search the <a href="https://www.encodeproject.org/search/?type=Experiment" target="_blank">ENCODE portal</a> for what you want, narrowing the results with the filters