a4bd219e77d824f808e182c7f1cc1881459dd381
lrnassar
  Wed Aug 4 13:08:16 2021 -0700
Adding references to the new filters quick start guide refs #24327

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 7106ea7..05f4982 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -4,59 +4,62 @@
 
 <!-- Relative paths to support mirror sites with non-standard GB docs install -->
 <!--#include virtual="$ROOT/inc/gbPageStart.html" -->
 
 <h1>Using UCSC Genome Browser Track Hubs</strong></h1>
 
 <h2>Contents</h2>
 
 <h6><a href="#Intro">What Are Track Hubs?</a></h6> 
 <h6><a href="#Assembly">What Are Assembly Hubs?</a></h6>
 <h6><a href="#View">Viewing Track Hubs</a></h6>
 <h6><a href="#Sharing">Sharing Track Hubs</a></h6>
 <h6><a href="#Setup">Setting up a Track Hub</a></h6>
 <h6><a href="#Debug">Debugging Track Hubs</a></h6>
 <h6><a href="#Search">Setting up item search</a></h6>
+<h6><a href="#Filters">Adding filters to your Track Hub</a></h6>
 <h6><a href="#Register">Registering a Track Hub with UCSC</a></h6>
 <h6><a href="#Compatibility">Checking Hub settings and compatibility</a></h6>
 <h6><a href="#Hosting">Where to host your data</a></h6>
 <hr>
 <p>
 <strong>Additional resources</strong></p> 
 <ul>
   <li>Raney BJ, et al. <a href="https://doi.org/10.1093/bioinformatics/btt637"
   target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on 
   the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. 
   <li> 
   <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hubs 
   Wiki</a></li> 
   <li>
   <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> 
   (Reference guide for trackDb parameter definitions)</li> 
   <li>
   <a href="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines" target="_blank">Public Hub 
   Guidelines Wiki</a></li> 
   <li>
   <a href="hubQuickStart.html" target="_blank">Quick Start Guide to Basic Hubs</a></li> 
   <li>
   <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into
   Groupings</a></li> 
   <li>
   <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs with 
   Blat</a></li> 
   <li><a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable Track 
   Hubs</a></li>
+  <li><a href="hubQuickStartFilter.html" target="_blank">Quick Start Guide to adding Filters to 
+  Hubs</a></li>
 </ul> 
 <div> 
 <form name="googleForm1" method="GET" action="http://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+'   site:genome.ucsc.edu/goldenPath/help';"> 
   <p>
   Search the Genome Browser help pages: &nbsp; 
   <input type="hidden" name="q" value=""> 
   <input type="hidden" name="num" value="10"> 
   <input type="hidden" name="filter" value="0"> 
   <input type=text name=qq size=30 maxlength=255 value=""> 
   <input type="submit" value="Submit"></p>
 </form> 
 </div> 
 <p> 
 <a href="../../contacts.html">Questions and feedback are welcome</a>.</p>
 
@@ -738,30 +741,45 @@
 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.soe.ucsc.edu/admin/exe/" target="_blank">here</a>. See an example
 <a href="examples/hubExamples/hubIndexedBigBedSearchable/" target="_blank">searchable hub</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>
+
 <!-- ========== Registering a Track Hub with UCSC ==================== -->
 <a name="Register"></a>
 <h2>Registering a Track Hub with UCSC</h2>
 <p>
 If you would like to share your track hub with other Genome Browser users, you can register your 
 hub with UCSC by contacting the Genome Browser technical support mailing list at 
 <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. Please include the URL of your 
 hub.txt file in the message. Once registered, your hub will appear as a link on the Public Hubs tab 
 on the Track Hubs page. To assist developers of Public Hubs, there is a 
 <a href="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines">Public Hubs Guidelines</a> 
 page. The page shares pointers and preferred style approaches, such as the need for creating 
 description html pages for your data that display any available references and an email contact for 
 further data questions.</p>
 <p>
 Alternatively, you can share your track hub with selected colleagues by providing them with the URL