4aca7440dcd66b53fa9b917d6fd3eae971924031 dschmelt Tue Jul 23 11:24:50 2019 -0700 Making style changes for CR #23857 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index d796f28..d5be6fa 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -638,75 +638,67 @@ reverse, and cross-species conversions, but does not accept batch input. The <a href="../cgi-bin/hgLiftOver">LiftOver</a> tool, accessed via the Tools link on the Genome 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: +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> +wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/liftOver</pre></li> <li>Change permissions on that file so that it can be executed <pre> -chmod +x liftOver -</pre></li> +chmod +x liftOver</pre></li> <li>Run the program with no arguments to see the usage statement <pre> -./liftOver -</pre> +./liftOver</pre> <pre> liftOver - Move annotations from one assembly to another usage: liftOver oldFile map.chain newFile unMapped -... -</pre></li> +...</pre></li> <li>Download your genome conversion chain file from the -<a href="http://hgdownload.cse.ucsc.edu/downloads.html">downloads directory</a>. + <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.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz</code> + <pre>wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.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". -<code> + 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 -</code></li> +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". + 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> +./liftOver preLift.bed hg19ToHg38.over.chain.gz conversions.bed unMapped</pre></li> </ol> -</p> - <a name="download33"></a> <h2>Linking gene name with accession number</h2> <h6>I have the accession number for a gene and would like to link it to the gene name. Is there a table that shows both pieces of information?</h6> <p> If you are looking at the RefSeq Genes, the <em>refFlat</em> table contains both the gene name (usually a HUGO Gene Nomenclature Committee ID) and its accession number. For the Known Genes, use the <em>kgAlias</em> table.</p> <a name="download31"></a> <h2>Obtaining a list of Known Genes</h2> <h6>How can I obtain a complete list of all the genes in the UCSC Known Genes table for a particular organism?</h6> <p>