84018a1d6515b75a60de04a61dd6f3f80be38580
brianlee
  Tue Jul 5 09:32:02 2022 -0700
Adding a link in hgTracksHelp.html, linked to from liftOver CGI, to a new anchor on FAQdownloads#liftOver that provides an example of running the command-line tool, refs #29698

diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html
index 819bcbf..641f166 100755
--- src/hg/htdocs/FAQ/FAQdownloads.html
+++ src/hg/htdocs/FAQ/FAQdownloads.html
@@ -645,30 +645,31 @@
 which is accessed from the View menu on the Genome Browser annotation tracks page, supports forward, 
 reverse, and cross-species conversions, but does not accept batch input. The 
 <a href="../cgi-bin/hgLiftOver">LiftOver</a> tool, accessed via the Tools link on the Genome 
 Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch 
 conversions.</p> 
 <p>
 If you wish to update a large number of coordinates to a different assembly and have access to a 
 Linux platform, you may find it useful to try the command-line version of the LiftOver tool. The 
 executable file for this utility can be downloaded 
 <a href="https://genome-store.ucsc.edu" target="_blank">here</a>. LiftOver requires a 
 pre-generated <em>over.chain</em> file as input, available for selected 
 assemblies from the 
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#liftover">Downloads</a> page. If the desired 
 file is not available, send a request to the <a href="../contacts.html">genome mailing list</a> and 
 we may be able to  provide you with one.</p>
+<h3 id="liftOver">Using liftOver</h3>
 <p>
 Here is an example on how to set up and run LiftOver from the command line:</p>
 <ol>
   <li>Download the LiftOver program for your computer's operating system 
 <a href="https://genome-store.ucsc.edu" target="_blank">here</a>
   <li>Change permissions on that file so that it can be executed
   <pre>
 chmod +x liftOver</pre></li>
   <li>Run the program with no arguments to see the usage statement
   <pre>
 ./liftOver</pre>
   <pre>
 liftOver - Move annotations from one assembly to another
 usage:
    liftOver oldFile map.chain newFile unMapped