64f5e1fb8b93253cf89a6f36fb00d67d2ededf1d gperez2 Sun Mar 15 20:52:02 2026 -0700 Updating the QuickLift documentation page and the Alignment Differences page, refs #35536 diff --git src/hg/htdocs/goldenPath/help/quickLiftChain.html src/hg/htdocs/goldenPath/help/quickLiftChain.html index f36c45f7f36..c3ffb71fa35 100644 --- src/hg/htdocs/goldenPath/help/quickLiftChain.html +++ src/hg/htdocs/goldenPath/help/quickLiftChain.html @@ -1,73 +1,98 @@ <h2>Description</h2> <p> -The Alignment Differences track shows mismatches and indels between the assembly from which the -track was QuickLifted and the current genome. +The Alignment Differences track shows mismatches, insertions, deletions, and double-sided +insertions between two assemblies. In <font color="#008000">QuickLift</font>, 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 currently viewing. +<font color="#008000">QuickLift</font> maps (liftOver) annotations on demand from the source +to the target using whole-genome alignment chains. </p> <h2>Display Conventions and Configuration</h2> <p> -Visible tracks, custom tracks, and track hubs on the Browser graphic page are carried over (lifted) -to the new assembly using the <font color="#008000">QuickLift</font> tracks checkbox. 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 new assembly. +This track is part of the <font color="#008000">QuickLift</font> track group, which appears +under a green "<font color="#008000">QuickLift</font> from ..." group in the target +genome assembly. <font color="#008000">QuickLift</font> tracks have a green left-side button +bar in the Browser graphic, instead of the usual gray, and can be removed by the +<button>Disconnect</button> button. </p> <p> -<font color="#008000">QuickLift</font> tracks appear under a green -"<font color="#008000">QuickLift</font> from ..." group in the New assembly. -<font color="#008000">QuickLift</font> tracks can be removed by the -<button>Disconnect</button> button. <font color="#008000">QuickLift</font> tracks have a green -left-side button bar in the Browser graphic, instead of the usual gray. -</p> -<p> -The "Alignment Differences" track displays liftOver differences using triangles and -lines; mousing over a triangle displays base-pair (bp) information. Lines and triangles are -color-coded as follows: +The Alignment Differences track displays liftOver differences using triangles and +lines. Alignment differences are marked by lines, with colored triangles indicating the type of +difference: </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></li> + <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> <div class="text-center"> <img src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'> </div> -<p>Clicking a triangle provides additional information about the alignment.</p> +<p> +Mousing over a triangle displays the size base-pair (bp) difference and the type of alignment +difference. 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> +<div class="text-center"> +<img src="../../images/QuickLift/quickLiftAlignmentDifferences.png" width='50%'> +</div> <h2>Methods</h2> <p> An alignment between two DNA sequences maps every nucleotide in one sequence to a nucleotide in another sequence. By making and using whole-genome alignments (Kent et al., 2003), genome annotations can be "lifted" 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. +(<a href="/cgi-bin/hgLiftOver" target="_blank">liftOver</a>) in bulk, one track at a time. +<font color="#008000">QuickLift</font> uses the same algorithm to lift 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. +</p> + +<p> +The Alignment Differences track is generated by comparing the whole-genome alignment chain between +the source and target assemblies. Where the alignment differs, the track classifies each +difference by type: </p> +<ul> + <li><b>Insertions and Deletions</b> — gaps in the alignment where one assembly has + sequence that the other does not</li> + <li><b>Double-sided insertions (double gaps)</b> — both assemblies contain + unalignable sequence between two aligned regions</li> + <li><b>Mismatches</b> — aligned positions where the bases differ between the two + assemblies</li> +</ul> <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, but we are working on making the pipeline to align two genomes more widely -available. +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> <h2>References</h2> <p> Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. <a href="https://www.pnas.org/doi/10.1073/pnas.1932072100?url_ver=Z39.88- 2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed" target="_blank"> Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes</a>. <em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a> </p>