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/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html
index dc4d18d..ad9451a 100755
--- src/hg/htdocs/FAQ/FAQformat.html
+++ src/hg/htdocs/FAQ/FAQformat.html
@@ -95,31 +95,33 @@
 Please note that only in custom tracks can the first lines of the file consist of header lines, 
 which begin with the word "browser" or "track" to assist the browser in the 
 display and interpretation of the lines of BED data following the headers. Such annotation track 
 header lines are not permissible in downstream utilities such as bedToBigBed, which convert lines of
 BED text to indexed binary files. </p>
 <P>
 If your data set is BED-like, but it is very large (over 50MB) and you would like to keep it on your
 own server, you should use the <a href="../goldenPath/help/bigBed.html">bigBed</a> data format.
 Read a <a href="https://genome-blog.soe.ucsc.edu/blog/2021/08/03/how-make-a-bigbed-file-part-1/"
 target="_blank">blog post</a> for step-by-step instructions.</p>
 <p>
 The first three required BED fields are: </p>
 <ol>
   <li> 
   <strong>chrom</strong> - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold 
-  (e.g.  scaffold10671).</li>
+  (e.g.  scaffold10671). Many assemblies also support several different
+  <a href="FAQcustom.html#custom12">chromosome aliases</a> (e.g. '1' or
+  'NC_000001.11' in place of 'chr1').</li>
   <li>
   <strong>chromStart</strong> - The starting position of the feature in the chromosome or scaffold. 
   The first base in a chromosome is numbered 0.</li>
   <li>
   <strong>chromEnd</strong> - The ending position of the feature in the chromosome or scaffold. The 
   <em>chromEnd</em> base is not included in the display of the feature, however,
   the number in <a href="FAQtracks#tracks1">position format</a> will be represented. For example,
   the first 100 bases of chromosome 1 are defined as <em>chrom=1, chromStart=0, chromEnd=100</em>,
   and span the bases numbered 0-99 in our software (not 0-100), but will represent the
   position notation chr1:1-100. Read more
   <a href="https://genome-blog.gi.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/">here</a>. 
   <br><em>chromStart</em> and <em>chromEnd</em> can be identical, creating a feature of length 0, commonly
   used for insertions. For example, use <em>chromStart=0, chromEnd=0</em> to represent an insertion before the
   first nucleotide of a chromosome.</li>
 </ol>