7af128b78ed12bb2c36df19130df47a09e03c41b dschmelt Fri Jul 19 16:01:51 2019 -0700 Adding info about liftOver #16541 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 621592b..d796f28 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -619,48 +619,94 @@ <td>X</td><td>X</td><td>X</td> </tr> <tr> <td>Y</td><td>Y</td><td>Y</td> </tr> </table> </div> </div> <a name="download28"></a> <h2>Converting genome coordinates between assemblies</h2> <h6>I've been researching a specific area of the human genome on the current assembly, and now you've just released a new version. Is there an easy way to locate my area of interest on the new assembly?</h6> <p> -You can migrate data from one assembly to another by using the <a href="../cgi-bin/hgBlat">blat</a> +You can migrate sequences from one assembly to another by using the <a href="../cgi-bin/hgBlat">Blat</a> alignment tool or by converting assembly coordinates. There are two conversion tools available on the Genome Browser web site: the Convert utility and the LiftOver tool. The Convert utility, -which is accessed from the menu on the Genome Browser annotation tracks page, supports forward, +which is accessed from the View menu on the Genome Browser annotation tracks page, supports forward, reverse, and cross-species conversions, but does not accept batch input. The -<a href="../cgi-bin/hgLiftOver">LiftOver</a> tool, accessed via the Utilities link on the Genome +<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 -UCSC-generated <em>over.chain</em> file as input. Pre-generated files are available for selected +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: +<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>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.cse.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> +</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> +chr1 11166587 11191615 MTOR +chr9 136130562 136150630 ABO +chr12 25358179 25403854 KRAS +chrX 151335633 151619831 GABRA3 +</code></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> +</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>