7835eff52a5b920e2ab64123fa72d1faf8f288f5 ann Fri Sep 13 14:46:35 2019 -0700 fixing two small bits diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index b996304..3ac3023 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -640,51 +640,47 @@ Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch conversions.</p> <p> If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool. The executable file for this utility can be downloaded <a href="https://genome-store.ucsc.edu" target="_blank">here</a>. LiftOver requires a pre-generated <em>over.chain</em> file as input, available for selected assemblies from the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#liftover">Downloads</a> page. If the desired file is not available, send a request to the <a href="../contacts.html">genome mailing list</a> and we may be able to provide you with one.</p> <p> Here is an example on how to set up and run LiftOver from the command line:</p> <ol> - <li>Download the LiftOver program for your computer's operating system. - <pre> -#For Linux computers -wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver -#For MacOS computers -wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/liftOver</pre></li> + <li>Download the LiftOver program for your computer's operating system +<a href="https://genome-store.ucsc.edu" target="_blank">here</a> <li>Change permissions on that file so that it can be executed <pre> chmod +x liftOver</pre></li> <li>Run the program with no arguments to see the usage statement <pre> ./liftOver</pre> <pre> liftOver - Move annotations from one assembly to another usage: liftOver oldFile map.chain newFile unMapped ...</pre></li> <li>Download your genome conversion chain file from the <a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads directory</a>. For example, the human to mouse conversion (hg38ToMm10) can be downloaded like so: - <pre>wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz</pre> + <pre>wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToMm10.over.chain.gz</pre> </li> <li>Prepare your BED file input. Here is a few lines from a BED file you can copy into a text file, saved as "preLift.bed". <pre> chr1 11166587 11191615 MTOR chr9 136130562 136150630 ABO chr12 25358179 25403854 KRAS chrX 151335633 151619831 GABRA3</pre></li> <li>You can now use the following command to LiftOver a BED file with annotations in your original genome, "preLift.bed", with your successful conversions in "conversions.bed" and unsuccessful conversions in "unMapped". <pre> ./liftOver preLift.bed hg19ToHg38.over.chain.gz conversions.bed unMapped</pre></li> </ol>