bbabbd5d2566d47d923d51dbe350634783455999
mspeir
  Sun Oct 26 12:14:52 2025 -0700
change soe to gi, refs #35031

diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html
index 35624070b35..5906707d80c 100755
--- src/hg/htdocs/goldenPath/help/bedMethyl.html
+++ src/hg/htdocs/goldenPath/help/bedMethyl.html
@@ -106,31 +106,31 @@
 
 
 <h2>Creating a bigMethyl custom track</h2>
 <a name="example2"></a>
 <h3>Example #2</h3>
 <p>
 In this example, you will create a bigMethyl file to display as a custom track.</p>
 <ol>
   <li>
   Save <a href="examples/bedMethyl.bed">this bedMethyl file</a> to your
   computer.</li>
   <li>
   Save the autoSql files <a href="examples/bigMethyl.as"><em>bigMethyl.as</em></a> to your computer.</li>
   <li>
   Download the <code>bedToBigBed</code>
-  <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utility</a>.</li>
+  <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">utility</a>.</li>
   <li>
 Use the <code>bedToBigBed</code> utility to create a bigMethyl file from your sorted bedMethyl file, using
 the <em>bedMethyl.bed</em> file and <em>chrom.sizes</em> files created above. </p>
 <pre><code><strong>bedToBigBed</strong> -as=bigMethyl.as -type=bed9+9 bedMethyl.bed https://genome.ucsc.edu/goldenPath/help/hg38.chrom.sizes bigMethyl.bb</code></pre></li>
 <p>
   <li>
 Move the newly created bigMethyl file (<em>bigMethyl.bb</em>) to a web-accessible http, https, or
 ftp location. At this point you should have a URL to your data, such as &quot;https://institution.edu/bigMethyl.bb&quot;, and the file should be accessible outside of your institution/hosting providers network. For more information on where to host your data, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation. Construct a custom track line with a bigDataUrl parameter pointing to the newly created bigMethyl file.</p>
   <pre><code>track type=bigMethyl name=&quot;bigMethyl Example&quot; description=&quot;A bigMethyl file&quot; bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb visibility=pack</code></pre></li>
   <li>
   Go to chr21:5,010,030-5,010,408 to see the data.</li>
 </ol>
 
 
 <a name=sharing_data></a>
@@ -140,39 +140,39 @@
 <a href="../../cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:5,010,030-5,010,408&hgct_customText=track%20type=bigMethyl%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb%20visibility=pack"
 target="_blank">This link</a> loads the same <em>bigMethyl.bb</em> track and sets additional display parameters from <a href="#example2">Example 2</a> in the URL:</p>
 <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:5,010,030-5,010,408&hgct_customText=track%20type=bigMethyl%20name=Example %20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb %20visibility=pack</code></pre>
 
 <p>
 If you would like to share your bigMethyl data track with a colleague, you can learn how to create
 a URL link to your data by looking at <a href="customTrack.html#EXAMPLE6">Example #6</a> on the
 custom track help page.</p>
 
 <a name=extracting_data></a>
 <h2>Extracting data from the bigMethyl format</h2>
 <p>
 Because the bigMethyl files are an extension of bigBed files, which are indexed binary files, it can
 be difficult to extract data from them. UCSC has developed the following programs to assist
 in working with bigBed formats, available from the
-<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p>
+<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">binary utilities directory</a>.</p>
 <ul>
   <li>
   <code>bigBedToBed</code> &mdash; converts a bigBed file to ASCII BED format.</li>
   <li>
   <code>bigBedSummary</code> &mdash; extracts summary information from a bigBed file.</li>
   <li>
   <code>bigBedInfo</code> &mdash; prints out information about a bigBed file.</li>
 </ul>
 <p>
 As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the
 command line to view the usage statement.</p>
 
 <a name=troubleshooting></a>
 <h2>Troubleshooting</h2>
 <p>
 If you encounter an error when you run the <code>bedToBigBed</code> program, check your input
 file for data coordinates that extend past the the end of the chromosome. If these are present, run
 the <code>bedClip</code> program
-(<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic
+(<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">available here</a>) to remove the problematic
 row(s) in your input file before running the <code>bedToBigBed</code> program.</p>
 
 
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