e2fa282b77b041b4acbdfb4644706c45828a2889
brianlee
  Thu Sep 12 15:31:24 2019 -0700
Linking to resources from chromEnd in BED FAQ format after MLQ email refs #24126

diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html
index cbba264..de88ecb 100755
--- src/hg/htdocs/FAQ/FAQformat.html
+++ src/hg/htdocs/FAQ/FAQformat.html
@@ -93,33 +93,36 @@
 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.</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>
   <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. For example, the first 100 
-  bases of a chromosome are defined as <em>chromStart=0, chromEnd=100</em>, and span the bases 
-  numbered 0-99.</li>
+  <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="http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/">here</a>.</li>
 </ol>
 <p>The 9 additional optional BED fields are:</p>
 <ol start=4>
   <li>
   <strong>name</strong> - Defines the name of the BED line. This label is displayed to the left of 
   the BED line in the Genome Browser window when the track is open to full display mode or directly 
   to the left of the item in pack mode.</li>
   <li>
   <strong>score</strong> - A score between 0 and 1000. If the track line <em>useScore</em> attribute
   is set to 1 for this annotation data set, the <em>score</em> value will determine the level of 
   gray in which this feature is displayed (higher numbers = darker gray). This table shows the 
   Genome Browser's translation of BED score values into shades of gray:
   <table>
     <tr>
       <td>shade</td>