9abe26a72523c34f65aa05a4dde5a9535b408e23
lrnassar
  Thu Jul 25 16:14:36 2019 -0700
Clarifying psl output to replicate web results #23814

diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html
index b94c8e1..94fad92 100755
--- src/hg/htdocs/FAQ/FAQblat.html
+++ src/hg/htdocs/FAQ/FAQblat.html
@@ -167,30 +167,33 @@
 Blat server on a separate port to enable translated Blat (protein searches or translated searches 
 in protein-space).</p>
 <p>
 <em>gfClient</em>:</p>
 <ul>
   <Li>Set <em>-minScore=0</em> and <em>-minIdentity=0</em>. This will result in some low-scoring, 
   generally spurious hits, but for interactive use it's sufficiently easy to ignore them (because 
   results are sorted by score) and sometimes the low-scoring hits come in handy.</li>
 </ul>
 <p>
 <em>standalone Blat</em>:</p>
 <ul>
   <li>Blat search:<br>
   &nbsp;&nbsp;&nbsp;<code>blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 
   database.2bit query.fa output.psl </code><br>
+  <li><strong>Note:</strong> To replicate web results, PSL output should be used. BLAT handles
+  alternative output formats (such as blast8) slightly differently, and this can lead to minor 
+  differences in results; particularly for short alignments.
 </ul>
 <p>
 Notes on repMatch:</p>
 <ul>
   <li>
   The default setting for gfServer dna matches is: repMatch = 1024 * (tileSize/stepSize).</li>
   <li>
   The default setting for Blat dna matches is: repMatch = 1024 (if tileSize=11).</li>
   <Li>To get command-line results that are equivalent to web-based results, repMatch must be 
   specified when using BLAT.</li>
 </ul>
 <p>
 For more information about how to replicate the score and percent identity matches displayed by our 
 web-based Blat, please see this <a href="../FAQ/FAQblat.html#blat4">BLAT FAQ</a>.</p>
 <p>