edb12b1895c6b72181ad7020eee9a6d52e49df74
mspeir
  Sun Jan 5 14:09:00 2025 -0800
Adding details about chromAlias stuff to various custom track pages, refs #26360

diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html
index 3564d75..8c6941b 100755
--- src/hg/htdocs/goldenPath/help/customTrackText.html
+++ src/hg/htdocs/goldenPath/help/customTrackText.html
@@ -42,31 +42,34 @@
   <li><a href="#TRACK">Track lines</a></li>
   <li>Data lines</li>
 </ul>
 
 <a name="CREATE"></a>
 <h3>Building and sharing a custom track</h3>
 <p>
 To construct an annotation file and display it in the Genome Browser, follow these steps:</p>
 
 <a name="format"></a>
 <p>
 <strong>Step 1. Format the data set</strong><br>
 Format your data as a tab-separated file using one of the
 <a href="/FAQ/FAQformat.html" target="_blank">formats supported</a> by the Genome
 Browser. You may include more than one data set in your
-annotation file; these need not be in the same format. Annotation data can be in a format designed
+annotation file; these need not be in the same format. For many formats,
+chromosome names can either be UCSC-style names (e.g. 'chr1', 'chrX')
+or <a href="/FAQ/FAQcustom.html#custom12">aliases</a> from other sources (e.g.
+'1' or 'NC_000001.11'). Annotation data can be in a format designed
 specifically for the Human Genome Project or UCSC Genome Browser, including:
 <div class="container">
   <div class="row">
     <div class="col-xs-12 col-sm-6 col-md-2">
       <ul>
         <li><a href="bedgraph.html">bedGraph</a>
         <li><a href="/FAQ/FAQformat.html#format4">GTF</a> and
             <a href="/FAQ/FAQformat.html#format3">GFF</a>
         <li><a href="/FAQ/FAQformat.html#format2">PSL</a>
         <li><a href="/FAQ/FAQformat.html#format1">BED</a>
         <li><a href="wiggle.html">WIG</a>
       </ul>
     </div>
     <div class="col-xs-12 col-sm-6 col-md-2">
       <ul>