ac55018f46e1dbfe5def208680bd30c25c8f27cc gperez2 Sat Mar 28 13:34:33 2026 -0700 Edits to the quickLift.html help page, refs #35536 diff --git src/hg/htdocs/goldenPath/help/quickLift.html src/hg/htdocs/goldenPath/help/quickLift.html index 12b8736cb60..04cbe751c94 100755 --- src/hg/htdocs/goldenPath/help/quickLift.html +++ src/hg/htdocs/goldenPath/help/quickLift.html @@ -1,157 +1,168 @@ <!DOCTYPE html> <!--#set var="TITLE" value="QuickLift Help" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> +<style>.quicklift { color: #008000; font-weight: bold; }</style> + <h1>QuickLift Help Page</h1> <!-- HREF paths are relative to cgi-bin, not goldenPath/help. --> -<a name="overview"></a> -<h3>Overview</h3> +<h2 id="overview">Overview</h2> <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 "lift" 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 +time. +</p> +<p> +<span class="quicklift">QuickLift</span> 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. +browsing a genome. For example, <span class="quicklift">QuickLift</span> can map annotations from +hg38 or hg19 to any of the hundreds of new human high-quality genomes in GenArk (HPRC), such as +viewing GENCODE genes from hg38 on a T2T assembly like hs1, with almost no additional delay. </p> <p> -<font color="#008000">QuickLift</font> functionality depends on the availability of alignment files +<span class="quicklift">QuickLift</span> 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> +<h2 id="gettingStarted">Getting Started</h2> <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: +To use <span class="quicklift">QuickLift</span>, 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 > 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> + from the top menu bar. + <div class="text-center"> + <img alt="The Convert page showing Source assembly (hg38), Destination with Search bar, Assembly dropdown, and QuickLift tracks checkbox" src="../../images/QuickLift/hgConvertV496.png" width="50%"> + </div> + </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 + chain available from your source assembly. 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> + <p><b>Note:</b> 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.</p> <div class="text-center"> - <img alt="Browser view showing QuickLift converted tracks from a different assembly" src="../../images/QuickLift/quickLiftTracks.png" width='50%'> + <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 - "<font color="#008000">QuickLift</font> from ..." group in the target - assembly. To remove <font color="#008000">QuickLift</font> tracks, click the - <button>Disconnect</button> button.</li> + <li>Click <button>Submit</button>. The results page will show the corresponding position(s) + in the target assembly with links to the Genome Browser. If any of your visible tracks + use a format not supported by <span class="quicklift">QuickLift</span>, the Convert page + will display a message: "Some of your tracks failed to lift because the type is not + supported by QuickLift." (See + <a href="#unsupportedTypes">Unsupported Track Formats</a> below.) + <p>If <span class="quicklift">QuickLift</span> was enabled, clicking a result link will + display your lifted tracks under a green + "<span class="quicklift">QuickLift</span> from ..." group in the target + assembly. To remove <span class="quicklift">QuickLift</span> tracks, click the + <button>Disconnect</button> button. This removes all + <span class="quicklift">QuickLift</span> tracks from the target assembly.</p></li> </ol> -<a name="visualIndicators"></a> -<h3>Visual Indicators</h3> +<h3 id="visualIndicators">Visual Indicators</h3> <p> -<font color="#008000">QuickLift</font> tracks have a green left-side button bar in the Browser +<span class="quicklift">QuickLift</span> 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%'> +<img alt="Green left-side button bar indicating QuickLift tracks in the Genome Browser" src="../../images/QuickLift/quickLiftGreenbuttons.png" width="7%"> </div> <p> -The Alignment Differences track displays liftOver differences using triangles and lines: +An <b>Alignment Differences</b> track also becomes available after running +<span class="quicklift">QuickLift</span>, displaying liftOver differences using colored 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> + <li>Insertions: <span style="color: #407F00; font-weight: bold;">green</span></li> + <li>Deletions: <span style="color: #00007F; font-weight: bold;">blue</span></li> + <li>Double-sided insertions: <span style="color: #7F7F7F; font-weight: bold;">gray</span> + (Both the source and target assemblies contain unalignable sequence between two + regions of aligned sequence)</li> + <li>Mismatches: <span style="color: #FF0000; font-weight: bold;">red</span></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%'> +<img alt="QuickLift Alignment Differences track showing colored triangle markers with mouseover tooltip displaying base-pair difference size and type" 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> +Clicking a triangle opens a details page showing: +</p> +<ul> + <li>Source and target assembly genome positions</li> + <li>DNA sequence alignment</li> + <li>Type and size of each alignment difference within the currently visible browser + region</li> +</ul> -<a name="unsupportedTypes"></a> -<h3>Unsupported Track Formats</h3> -<p><font color="#008000">QuickLift</font> does not support the following track formats:</p> +<h2 id="unsupportedTypes">Unsupported Track Formats</h2> +<p><span class="quicklift">QuickLift</span> does not support the following track formats:</p> <ul> <li>WIG — <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 — <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 — <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 & Support</h3> +<h2 id="resources">Resources & Support</h2> <ul> <li><a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver</a> — convert coordinates or annotation files in bulk between assemblies</li> <li><a href="/goldenPath/help/chain.html" target="_blank">Chain format</a> — description of the alignment chain files used by - <font color="#008000">QuickLift</font> and liftOver</li> + <span class="quicklift">QuickLift</span> and liftOver</li> <li><a href="/contacts.html" target="_blank">Contact us</a> — request a new liftOver chain or report issues via the genome mailing list</li> </ul> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->