094c4d429df5c052a59dc6414e948f31e3f8d9ee hiram Tue Jan 20 12:00:18 2026 -0800 grammar correction from code review refs #36974 diff --git src/hg/htdocs/liftRequest.html src/hg/htdocs/liftRequest.html index 822307541a4..bc0f58ac586 100755 --- src/hg/htdocs/liftRequest.html +++ src/hg/htdocs/liftRequest.html @@ -1,122 +1,122 @@ <!DOCTYPE HTML> <!--#set var="TITLE" value="Genome Assembly Alignment Request" --> <!--#set var="ROOT" value="" --> <!--#include virtual='$ROOT/inc/gbPageStartHardcoded.html' --> <link rel='stylesheet' type='text/css' href="<!--#echo var='ROOT' -->/style/jquery-ui.css"> <link rel='stylesheet' type='text/css' href="<!--#echo var='ROOT' -->/style/HGStyle.css"> <link rel='stylesheet' type='text/css' href="<!--#echo var='ROOT' -->/style/liftRequest.css"> <div id="formContainer" class="form-container"> <h1>Genome Assembly Alignment Request</h1> <p> On this page you can request a whole-genome alignment between two genomes that are on the UCSC Genome Browser. Such alignments can take thousands of compute hours to produce. The alignment here will be generated on the <a href='https://usegalaxy.org/' target=_blank>Galaxy</a> platform, using a workflow that uses the <a href='https://tacc.utexas.edu/' target=_blank>TACC</a></a> high performance compute GPU resources. The full process may take up to a few days. You will receive an email when it is complete. </p> <p> - Once complete, your will find two new tracks on both assemblies, one with + Once complete, you will find two new tracks on both assemblies, one with the full alignment results ("all chains"), and one track with the best alignment (single coverage) for every basepair, which can be used for "liftOver". Since these tracks are single-coverage on the current genome, the alignments are reciprocal so one is produced per assembly. For more information on how to download these chain files and use liftOver, see also: <a href='https://genome.ucsc.edu/FAQ/FAQdownloads.html#download28' target=_blank>Converting coordinates</a>. Once these tracks are available, you can also use our Quicklift feature to lift annotations on-the-fly, as you use the browser, see also: <a href='https://docs.google.com/document/d/1wecESHUpgTlE6U_Mj0OnfHeSZBrTX9hkZRN5jlJS8ZQ/edit?usp=sharing' target=_blank>Quick Lift guide</a> for more information. </p> <p>If one of the two genomes is not on the UCSC browser yet, please request it first on our <a href="https://genome.ucsc.edu/assemblySearch.html" target=_blank>Assembly Request Page</a>, then come back here when the assembly has been added to the browser. </p> <div class="form-group"> <label for="genomeSearch1">Assembly 1</label> <div class="assembly-input-wrapper"> <input id="genomeSearch1" type="text" placeholder="Search any species, genome or assembly name" autocomplete="off"> <input id="genomeSearchButton1" value="Search" type="button"> </div> <div id="genomeLabel1" class="selected-assembly">No assembly selected</div> </div> <div class="form-group"> <label for="genomeSearch2">Assembly 2</label> <div class="assembly-input-wrapper"> <input id="genomeSearch2" type="text" placeholder="Search any species, genome or assembly name" autocomplete="off"> <input id="genomeSearchButton2" value="Search" type="button"> </div> <div id="genomeLabel2" class="selected-assembly">No assembly selected</div> </div> <div id="liftExists" class="form-group" style="display: none;"> <button id="dismissLiftExists" style="float: right; cursor: pointer;">×</button> <div class="description"> <p><strong>LiftOver chain files already exist for these assemblies:</strong></p> <p> <strong>Assembly 1:</strong> <a id="genome1Link" href="#" target="_blank"></a> browser link<br> Download: <a id="genome1LiftOver" href="#" download>Download chain file</a> over.chain.gz file </p> <p> <strong>Assembly 2:</strong> <a id="genome2Link" href="#" target="_blank"></a> browser link<br> Download: <a id="genome2LiftOver" href="#" download>Download chain file</a> over.chain.gz file </p> </div> </div> <div id="emailForm" class="form-group"> <label for="emailInput">Email Address</label> <div class="description">You will receive a notification at this address when the alignment is complete.</div> <input id="emailInput" type="email" placeholder="your.email@example.com"> </div> <div id="commentsForm" class="form-group"> <label for="commentsInput">Comments (optional)</label> <div class="description">Any additional information or notes about this alignment request.</div> <textarea id="commentsInput" placeholder="Enter any additional information here..."></textarea> </div> <div id="submitButton" class="form-group"> <input id="submitBtn" type="button" value="Submit Request" onclick="submitForm()"> </div> </div> <!-- end of formContainer --> <div id="successMessage"> <h2>Your request has been submitted, you will receive an email when the alignment is complete.</h2> <a href="<!--#echo var='ROOT' -->/cgi-bin/hgGateway">Back to the genome browser gateway page</a> </div> <div id="errorMessage"> <h3>Error</h3> <p id="errorText"></p> </div> <hr /> </div><!-- closing gbsPage from gbPageStartHardcoded.html --> </div><!-- closing container-fluid from gbPageStartHardcoded.html --> <!--#include virtual="$ROOT/inc/gbFooterHardcoded.html"--> <script src="<!--#echo var='ROOT' -->/js/jquery.js"></script> <script src="<!--#echo var='ROOT' -->/js/jquery.plugins.js"></script> <script src="<!--#echo var='ROOT' -->/js/utils.js"></script> <script src="<!--#echo var='ROOT' -->/js/jquery-ui.js"></script> <script src="<!--#echo var='ROOT' -->/js/autocompleteCat.js"></script> <script src="<!--#echo var='ROOT' -->/js/liftRequest.js"></script> </body></html>