84018a1d6515b75a60de04a61dd6f3f80be38580 brianlee Tue Jul 5 09:32:02 2022 -0700 Adding a link in hgTracksHelp.html, linked to from liftOver CGI, to a new anchor on FAQdownloads#liftOver that provides an example of running the command-line tool, refs #29698 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 3ce735e..669993a 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1249,31 +1249,33 @@ liftOver does not return a match if the region is split in the new assembly. Consider checking this option for conversions involving high-quality data within the same species. This option should not be used when mapping large regions, doing cross-species conversions or using fragmented poor-quality assemblies. <li><strong>Min ratio of alignment blocks/exons that must map</strong> (default 1)<strong>:</strong> <li><strong>If thickStart/thickEnd is not mapped, use the closest mapped bas</strong> (default off)<strong>:</strong> </ul> --> <h3>Command-line coordinate lifting</h3> <p> The command-line version of liftOver offers the increased flexibility and performance gained by -running the tool on your local server. This utility requires access to a Linux platform. The +running the tool on your local server. See an example of running the liftOver tool +<a href="../../FAQ/FAQdownloads.html#liftOver">here</a>. +This utility requires access to a Linux platform. The executable file may be downloaded <a href="https://genome-store.ucsc.edu">here</a>. Command-line liftOver requires a UCSC-generated <em>over.chain</em> file as input. Pre-generated files for a given assembly can be accessed from the assembly's "LiftOver files" link on the <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page. If the desired conversion file is not listed, send a request to the <a href="../../contacts.html">genome mailing list</a> and we may be able to generate one for you. For use of the command-line version of LiftOver, we require all for-profit businesses or commercial companies to <a href="https://genome-store.ucsc.edu/">purchase a license</a> to support our small team.</p> <a name="Download"></a> <h2>Downloading genome data</h2> <p> Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. All of the tables are freely usable for any purpose except as indicated in the README.txt file in the download directories. This data was contributed by many