048b2becc526e0ec8ef7d4a172543349e72d2020
mspeir
  Mon Jan 27 10:00:50 2025 -0800
adding pointers to net construction example in GenomeWiki, refs #26358

diff --git src/hg/htdocs/FAQ/FAQtracks.html src/hg/htdocs/FAQ/FAQtracks.html
index 8602f018684..f0b01a38956 100755
--- src/hg/htdocs/FAQ/FAQtracks.html
+++ src/hg/htdocs/FAQ/FAQtracks.html
@@ -20,30 +20,31 @@
 <li><a href="#tracks6">Evaluating possible alternative splices</a></li>
 <li><a href="#tracks7">Matching exons and protein sequence</a></li>
 <li><a href="#tracks9">Cause of duplicated gene</a></li>
 <li><a href="#tracks11">Protein doesn't begin with methionine</a></li>
 <li><a href="#tracks12">Doing an orthology track analysis of a protein</a></li>
 <li><a href="#tracks14">Quality benchmarks for predicted genes</a></li>
 <li><a href="#tracks15">Display conventions for gene prediction tracks</a></li>
 <li><a href="#tracks16">Viewing detailed displays in conservation tracks</a></li>
 <li><a href="#tracks17">Negative strand coordinates in PSL files</a></li>
 <li><a href="#tracks18">Inconsistency in stop codon treatment in GTF tracks</a></li>
 <li><a href="#tracks19">Obtaining clones referenced in Genome Browser</a></li>
 <li><a href="#tracks20">Locating centromeres and telomeres</a></li>
 <li><a href="#tracks21">Determining the table name for an annotation track</a></li>
 <li><a href="#tracks22">Unexpected results in UCSC RefSeq track</a></li>
 <li><a href="#tracks23">What is the difference between super tracks and composite tracks?</a></li>
+<li><a href="#tracks24">Constructing nets from chains</a></li>
 </ul>
 <hr>
 <p>
 <a href="index.html">Return to FAQ Table of Contents</a></p>
 
 <a name="speed"></a>
 <h2>Why is my tracks display slow?</h2>
 <p>
 There are different reasons why the Genome Browser tracks display can become slow. 
 Below is a list of common scenarios alongside potential solutions. The most common
 reason involves the configuration settings that are saved as users interact with
 the Genome Browser, such as track visibilities and custom data. 
 This can be solved by a reset of all your current Genome Browser session
 information although it is important to note that this will reset all
 settings including filters, track order and remove all custom data. To do
@@ -483,16 +484,28 @@
     ...
        track subTrack_1_NameIncomposite
        parent compositeTrackNameInSuperTrack on
        ...
        track subTrack_2_NameIncomposite
        parent compositeTrackNameInSuperTrack off
 </code></pre></p>
 <p><b>Key Differences</b>:</p>
 <ul>
  <li>Composite Tracks: Group similar subtracks in a single level with visibility set per track using [on/off].</li>
  <li>Supertracks: Group diverse tracks (including composite tracks) in a two level of hierarchy with visibility set
      separately for each subtrack.</li>
 </ul>
 <p>For more information about superTracks and composite tracks, refer to the
 <a href="../goldenPath/help/hubQuickStartGroups" target="_blank">Organizing Track Hubs into Groupings help page</a>.</p> 
+
+<a name="tracks24"></a>
+<h2>Constructing nets from chains</h2>
+<h6>How are nets constructed from pairwise alignment chains?</h6>
+<p>
+In short, nets are constructed to be single-coverage on the target assembly.
+Nets are constructed from whole or parts of chains based on score. More details
+can be found in this
+<a href="https://genomewiki.ucsc.edu/index.php?title=Chains_Nets#Net_construction_example"
+target="_blank">net construction example</a> in our wiki.
+
+
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