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

diff --git src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
index b4f83f83e0d..fd09eb8d590 100755
--- src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
+++ src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
@@ -29,47 +29,47 @@
 <p>
 Download some example GFF3 data from Gencode. This file happens to be long non-coding RNAs (lncRNAs):
 <pre><code>wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.long_noncoding_RNAs.gff3.gz</code></pre></p>
 <p>
 Next, you will need to download four Genome Browser utilities to convert the GFF3 file to 
 bigBed format and run the search index command. Similar commands exist to convert other file types.
 These are operating system specific:
 <table>
   <tr>
     <th>Utility Name</th>
     <th>MacOS Download</th>
     <th>Linux Download</th>
   </tr>
   <tr>
     <td>gff3ToGenePred</td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/gff3ToGenePred">Download</a></td>
-    <td style="text-align:center"style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/macOSX.x86_64/gff3ToGenePred">Download</a></td>
+    <td style="text-align:center"style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred">Download</a></td>
   </tr>
   <tr>
     <td>genePredToBed</td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/genePredToBed">Download</a></td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBed">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/macOSX.x86_64/genePredToBed">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/linux.x86_64/genePredToBed">Download</a></td>
   </tr>
   <tr>
     <td>bedToBigBed</td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/bedToBigBed">Download</a></td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/macOSX.x86_64/bedToBigBed">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed">Download</a></td>
   </tr>
   <tr>
     <td>IxIxx</td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/ixIxx">Download</a></td>
-    <td style="text-align:center"><a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ixIxx">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/macOSX.x86_64/ixIxx">Download</a></td>
+    <td style="text-align:center"><a href="http://hgdownload.gi.ucsc.edu/admin/exe/linux.x86_64/ixIxx">Download</a></td>
   </tr>
 </table>
 </p>
 <h3>STEP 2: Format Data</h3> 
 <p>
 In order to format the data, you will need to run a command to make those commands executable:</p>
 <pre><code>chmod +x gff3ToGenePred genePredToBed bedToBigBed IxIxx</code></pre>
 
 <p>
 Then run the first conversion from GFF3 to genePred, making sure to include
 <code>-geneNameAttr=gene_name</code> so that gene symbol is used as the name2 instead of
 ID number, and sorting by chromosome and position:</p>
 <pre><code>gff3ToGenePred -geneNameAttr=gene_name gencode.v32.long_noncoding_RNAs.gff3.gz stdout | sort -k2,2 -k4n,4n > gencode.v32.lncRNAs.genePred</code></pre>
 
 <p>