1c6f1b10ac6d787712552650182fe1409f83d33d gperez2 Wed Feb 25 13:42:59 2026 -0800 Code review edit, refs #37147 diff --git src/hg/htdocs/goldenPath/help/quickLiftChain.html src/hg/htdocs/goldenPath/help/quickLiftChain.html index 44e21101257..f36c45f7f36 100644 --- src/hg/htdocs/goldenPath/help/quickLiftChain.html +++ src/hg/htdocs/goldenPath/help/quickLiftChain.html @@ -1,72 +1,73 @@ <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. </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. </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: </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> <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> <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. </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, but we are working on making the pipeline to align two genomes more widely available. </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>