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 @@ XXX YYY

Converting genome coordinates between assemblies

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?

-You can migrate data from one assembly to another by using the blat +You can migrate sequences from one assembly to another by using the Blat 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 -LiftOver tool, accessed via the Utilities link on the Genome +LiftOver 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.

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 here. LiftOver requires a -UCSC-generated over.chain file as input. Pre-generated files are available for selected +pre-generated over.chain file as input, available for selected assemblies from the Downloads page. If the desired file is not available, send a request to the genome mailing list and we may be able to provide you with one.

+

+Here is an example on how to set up and run LiftOver from the command line: +

    +
  1. Download the LiftOver program for your computer's operating system. +
    +#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
+
    2. +
  2. Change permissions on that file so that it can be executed +
    +chmod +x liftOver
+
    3. +
  3. Run the program with no arguments to see the usage statement +
    +./liftOver
+
    +
    +liftOver - Move annotations from one assembly to another
+usage:
+   liftOver oldFile map.chain newFile unMapped
+...
+
    4. +
  4. Download your genome conversion chain file from the +downloads directory. +For example, the human to mouse conversion (hg38ToMm10) can be downloaded like so: +
    wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
+
    5. +
  5. 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". + +chr1 11166587 11191615 MTOR +chr9 136130562 136150630 ABO +chr12 25358179 25403854 KRAS +chrX 151335633 151619831 GABRA3 +
    6. +
  6. 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". +
    +./liftOver preLift.bed hg19ToHg38.over.chain.gz conversions.bed unMapped
+
    7. +
+

+

Linking gene name with accession number

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?

If you are looking at the RefSeq Genes, the refFlat table contains both the gene name (usually a HUGO Gene Nomenclature Committee ID) and its accession number. For the Known Genes, use the kgAlias table.

Obtaining a list of Known Genes

How can I obtain a complete list of all the genes in the UCSC Known Genes table for a particular organism?