a555f913f8ea500e670e38d03a365ea7c1426fa9 dschmelt Wed Jan 19 17:32:57 2022 -0800 Documenting liftOver file size limit part A of refs #28765 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index ce7fc7a..4efee41 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1148,53 +1148,56 @@ and coordinate lifting. The BLAT alignment tool is described in the section <a href="#BLATAlign">Using BLAT alignments</a>.</p> <h3>Coordinate conversion</h3> <p> The Genome Browser Convert utility is useful for locating the position of a feature of interest in a different release of the same genome or (in some cases) in a genome assembly of another species. During the conversion process, portions of the genome in the coordinate range of the original assembly are aligned to the new assembly while preserving their order and orientation. In general, it is easier to achieve successful conversions with shorter sequences.</p> <p> When coordinate conversion is available for an assembly, click on the "View" pulldown on the top blue menu bar on the Genome Browser page and select the "In Other Genomes (Convert)" link. You will be presented with a list of the genome/assembly conversion options available for the current assembly. Select the genome and assembly to which you'd like to convert -the coordinates, then click the Submit button. If the conversion is successful, the browser will +the coordinates, then click the <button>Submit</button> button. If the conversion is successful, + the browser will return a list of regions in the new assembly, along with the percent of bases and span covered by that region. Click on a region to display it in the browser. If the conversion is unsuccessful, the utility returns a failure message.</p> <a name="Liftover"></a> <h3>Lifting coordinates</h3> <p> The liftOver tool is useful if you wish to convert a large number of coordinate ranges between assemblies. This tool is available in both web-based and command line forms, and supports forward/reverse conversions as well as conversions between species. You can use the <a href="../../FAQ/FAQformat.html#format1">BED format</a> (e.g. "chr4 100000 100001", 0-based) or directly paste text from the position box ("chr4:100,001-100,001", 1-based). See our <a href="http://genome.ucsc.edu/blog/patches/">Coordinate Counting</a> blog post for a discussion of the difference. If the coordinates do not cover a single base pair e.g. "chr4 100000 100000" (BED) or "chr4:100,001-100,000" (text), this tool automatically extends them to at least one base pair.</p> <h3>Web-based coordinate lifting</h3> <p> To access the graphical version of the liftOver tool, click on "Tools" pulldown in the top blue menu bar of the Genome Browser, then select -<a href="http://genome.ucsc.edu/cgi-bin/hgLiftOver">LiftOver</a> from the menu.</p> +<a href="http://genome.ucsc.edu/cgi-bin/hgLiftOver">LiftOver</a> from the menu. +Note that the web tool has an input file size limit of 500Mb, larger files will require +using the command-line version.</p> <p> To convert one or more coordinate ranges using the default conversion settings:</p> <ol> <li> Select the genome and assembly from which the ranges were taken ("Original"), as well as the genome and assembly to which the coordinates should be converted ("New").</li> <li> Select the Data Format option: Browser Extensible Data format (<a href="../../FAQ/FAQformat.html#format1">BED</a>) or position (coordinates of the form <em>chrN:start-end</em>).</li> <li> Enter coordinate ranges in the selected data format into the large text box, one per line.</li> <li> Click Submit.</li> </ol> @@ -1228,31 +1231,33 @@ 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 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.</p> +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 researchers, as listed on the Genome Browser <a href="../credits.html" target="_blank">Credits</a> page. Please acknowledge the contributor(s) of the data you use. <h3>Downloading the data</h3> <p> Genome data can be downloaded in different ways using our North American and European download servers, hgdownload, hgdownload2, and hgdownload-euro.</p> <dl>