d5932e4051a4885f0036831cdfc5fbf1eb08a499 lrnassar Tue Oct 10 17:16:27 2023 -0700 Fixing broken blog links, refs #32439 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index a7303ee..9ea6990 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1217,31 +1217,31 @@ available for the current assembly. Select the genome and assembly to which you'd like to convert 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 +See our <a href="https://genome-blog.gi.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> <p> <b>Note:</b> It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following <a href="/FAQ/FAQreleases.html#snpConversion">FAQ entry</a>.</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. Note that the web tool has an input file size limit of 500Mb, larger files will require using the command-line version.</p>