019256d07c6f791954ecb76e3e40a4da960098ef
lrnassar
  Wed Mar 18 16:43:19 2026 -0700
Fixing small issues I noticed in commits, refs #37243

diff --git src/hg/htdocs/goldenPath/help/hgConvert.html src/hg/htdocs/goldenPath/help/hgConvert.html
index 58d24052dcf..3a1fc2cef2e 100755
--- src/hg/htdocs/goldenPath/help/hgConvert.html
+++ src/hg/htdocs/goldenPath/help/hgConvert.html
@@ -1,147 +1,146 @@
-<!-- This file is included in hgVai's "Using the Variant Annotation Integrator" section. -->
 <!-- HREF paths are relative to cgi-bin, not goldenPath/help. -->
 
 <a name="overview"></a>
 <h3>Overview</h3>
 <p>
 An alignment between two DNA sequences maps every nucleotide in one sequence to a nucleotide in
 another sequence. By making and using
 <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC208784/" target="_blank">whole-genome alignments</a>,
 the UCSC Genome Browser always allowed users to &quot;lift&quot; genome annotations to another
 assembly (<a href="/cgi-bin/hgLiftOver" target="_blank">liftOver</a>), in bulk, one track at a
 time. <font color="#008000">QuickLift</font> is a tool that uses the same algorithm, but it maps
 (liftOver) annotations on demand, in real-time, for all visible tracks. Only the
 annotations in the currently visible region are lifted, so this is usually fast enough when
 browsing a genome. For example, <font color="#008000">QuickLift</font> can be used to map
 annotations from hg38 or hg19 to any of the hundreds of new human high-quality genomes in GenArk
 (HPRC), with almost no additional delay. For instance, you can view GENCODE genes from hg38
 on a T2T assembly like hs1, carrying over your visible tracks to the target genome assembly.
 </p>
 <p>
 <font color="#008000">QuickLift</font> functionality depends on the availability of alignment files
 (chains) that describe how sequences in one assembly correspond to another. The alignment files are
 currently made at UCSC, and if no alignment file is available for the assembly in which you're
 interested, please send a request to the <a href="/contacts.html" target="_blank"
 >genome mailing list</a>, and we will attempt to provide you with one.
 </p>
 
 <a name="gettingStarted"></a>
 <h3>Getting Started</h3>
 <p>
 The <b>source assembly</b> is the assembly where the annotations come from, and the
 <b>destination (target) assembly</b> is the assembly you are converting to.
 To use <font color="#008000">QuickLift</font>, follow these steps:
 </p>
 <ol>
     <li>Navigate to the genome assembly and position you want to convert in the
         <a href="/cgi-bin/hgTracks" target="_blank">Genome Browser</a>. Make sure the
         tracks you want to lift are visible.</li>
     <li>Open the Convert page by going to <b>View &gt; In Other Genomes (Convert)</b>
         from the top menu bar, or navigate directly to
         the <a href="/cgi-bin/hgConvert" target="_blank">Convert page</a>.</li>
     <li>Under <b>Destination</b>, choose the target genome assembly. You can either:
         <ul>
             <li>Use the <b>Search</b> bar to find a target genome by name. As you type,
                 an autocomplete dropdown appears with matching genomes. The search
                 automatically filters results to show only assemblies that have a liftOver
                 chain available from your source assembly. Genomes without an available
                 liftOver chain are excluded from the results. You can also click the
                 dropdown toggle button to browse recent and popular genomes.</li>
             <li>Use the <b>Assembly</b> dropdown to select from other assemblies
                 of the same organism (e.g., other human assemblies when the source assembly is
                 hg38). To convert to a different organism, use the Search bar
                 instead.</li>
         </ul>
     </li>
     <li>Check the <b>QuickLift tracks</b> checkbox to carry over your visible tracks,
         custom tracks, and track hubs to the target assembly. Without this checkbox, only the
         coordinate position is converted.
         <ul>
             <li>When a single track from a container track, such as a superTrack or
                 composite, is lifted, the entire container track is carried over to the
                 target genome assembly.</li>
         </ul>
         <div class="text-center">
         <img alt="Browser view showing QuickLift converted tracks from a different assembly" src="../../images/QuickLift/quickLiftTracks.png" width='50%'>
         </div>
     </li>
     <li>Click <b>Submit</b>. The results page will show the corresponding position(s)
         in the target assembly with links to the Genome Browser. If
         <font color="#008000">QuickLift</font> was enabled, clicking a link will display your
         lifted tracks under a green
         &quot;<font color="#008000">QuickLift</font> from ...&quot; group in the target
         assembly. To remove <font color="#008000">QuickLift</font> tracks, click the
         <button>Disconnect</button> button.</li>
 </ol>
 
 <a name="visualIndicators"></a>
 <h3>Visual Indicators</h3>
 <p>
 <font color="#008000">QuickLift</font> tracks have a green left-side button bar in the Browser
 graphic (instead of the usual gray):
 </p>
 <div class="text-center">
 <img alt="Green QuickLift buttons used to convert coordinates between assemblies" src="../../images/QuickLift/quickLiftGreenbuttons.png" width='7%'>
 </div>
 <p>
 The Alignment Differences track displays liftOver differences using triangles and lines:
 </p>
               <ul>
 		<li>Insertions: <font color="#407F00">green</font></li>
 		<li>Deletions: <font color="#00007F">blue</font></li>
 		<li>Double-sided insertions: <font color="#7F7F7F">gray</font> (Both the source
 		and target assemblies contain unalignable sequence between two regions of aligned
 		sequence)</li>
 		<li>Mismatches: <font color="#FF0000">red</font></li>
               </ul>
 <p>
 Mousing over a triangle displays the size base-pair (bp) difference and the type of alignment
 difference.
 </p>
 <div class="text-center">
 <img alt="QuickLift track with triangle markers indicating alignment differences on mouseover" src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'>
 </div>
 <p>
 Clicking a triangle provides the source and target assembly genome positions, DNA sequence
 alignment, including the type of alignment difference with the bases within the currently
 visible browser region.</p>
 
 <a name="unsupportedTypes"></a>
 <h3>Unsupported Track Formats</h3>
 <p><font color="#008000">QuickLift</font> does not support the following track formats:</p>
       <ul>
         <li>WIG &mdash; <a href="/goldenPath/help/bigWig.html" target="_blank">bigWig</a>
             is supported; WIG tracks can be converted to bigWig using the
             <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>wigToBigWig</code></a>
             utility</li>
         <li>BAM</li>
 	<li>CRAM</li>
         <li>PSL &mdash; <a href="/FAQ/FAQformat.html#format1" target="_blank">BED</a>
             is supported; PSL tracks can be converted to BED using the
             <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>pslToBed</code></a>
             utility</li>
         <li>VCF</li>
         <li>HIC</li>
         <li>MAF</li>
         <li>bigChain</li>
         <li>Interact</li>
         <li>narrowPeak / broadPeak &mdash;
             <a href="/goldenPath/help/bigBed.html" target="_blank">bigBed</a>
             is supported; since narrowPeak and broadPeak are BED-based formats, they can be
             converted to bigBed using the
             <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>bedToBigBed</code></a>
             utility</li>
         <li>pgSnp</li>
       </ul>
 
 <a name="resources"></a>
 <h3>Resources &amp; Support</h3>
 <ul>
     <li><a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver</a> &mdash; convert
         coordinates or annotation files in bulk between assemblies</li>
     <li><a href="/goldenPath/help/chain.html" target="_blank">Chain format</a> &mdash;
         description of the alignment chain files used by
         <font color="#008000">QuickLift</font> and liftOver</li>
     <li><a href="/contacts.html" target="_blank">Contact us</a> &mdash; request a new
         liftOver chain or report issues via the genome mailing list</li>
 </ul>