dd05936cd30e6438d5085146d9d843047739f63e
gperez2
  Fri Jan 9 16:00:19 2026 -0800
Updating and adding extraIndex and searchIndex documentation to the track hubs help page, refs #19337

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 31bcc332a95..2a927167a16 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -1062,34 +1062,40 @@
 <!-- ========== Setting Up Track Item Search ============================== -->
 <a name="Search"></a>
 <h2>Setting up track item search</h2>
 <p> 
 The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support 
 this behavior you have to add an index to the bigBed file when you initially create the the bigBed 
 file from the bed file input. Indices are usually created on the name field of the bed, but can be 
 created on any field of the bed. Free-text searches can also be enabled by creating a 
 <a href="trix.html">TRIX index file</a> that maps id's in the track to free-text metadata. Further
 instructions can be found in the <a href="hubQuickStartSearch.html">Searchable Hub Quick Start 
 Guide</a>.</p>
 <p>
 See the searchIndex and searchTrix fields in the <a href="trackDb/trackDbHub.html">Hub Track 
 Database Definition document</a> for 
 information on how to set up your bigBed to enable searching. The searchIndex setting requires
-the input BED data to be case-senstive sorted (<code>sort -k1,1 -k2,2n</code>). You can use
-either the example UNIX <code>sort</code> command or the <code>bedSort</code> utility available
-<a href="http://hgdownload.gi.ucsc.edu/admin/exe/" target="_blank">here</a>. See an example
-<a href="examples/hubExamples/hubIndexedBigBedSearchable/" target="_blank">searchable hub</a>.</p>
+the input BED data to be case-sensitive sorted (<code>sort -k1,1 -k2,2n</code>), which can be done
+using the <code>-sort</code> option in the <a href="http://hgdownload.gi.ucsc.edu/admin/exe/"
+target="_blank">bedToBigBed utility</a>.</p>
+<p>
+When a bigBed file is used in a track hub, additional indices can be created to support searching
+on specific fields. For example, running <code>bedToBigBed</code> with <code>-extraIndex=name</code>
+builds an index on the name field. You can then enable searching on that field by adding:</p>
+<pre><code>searchIndex name</code></pre>
+<p>to the stanza for that bigBed track in the hub's trackDb.txt file. See the
+<a href="examples/hubExamples/hubIndexedBigBedSearchable/" target="_blank">searchable hub example</a>.</p>
 
 <!-- ========== Adding Filters to Track Hub ============================== -->
 <a name="Filters"></a>
 <h2>Adding Filters to your Track Hub</h2>
 <p>
 The Genome Browser supports three varieties of data filter options for bigBed data.
 These can improve data usability in many ways, such as displaying specific data by default 
 (e.g. only items that pass certain quality scores), allow for filtering based on 
 pre-specified categories (e.g designate only LINE repetitive elements from a list of options) 
 and more.</p>
 <p>
 For more information on the options available and examples on how to set up filters, see our
 <a href="hubQuickStartFilter.html" target="_blank">Track Hub Filters Quick Start Guide</a>
 and the filter entries in the <a href="trackDb/trackDbHub.html#filter" target="_blank">
 Track Database Definition Document</a>.</p>