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

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
-

Change permissions on that file so that it can be executed
```
-chmod +x liftOver
-
```

Run the program with no arguments to see the usage statement

-./liftOver
-

+./liftOver

 liftOver - Move annotations from one assembly to another
 usage:
    liftOver oldFile map.chain newFile unMapped
-...
-

Download your genome conversion chain file from the -downloads directory. + 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
+  wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

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". -+ 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
-
```
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".
```
-./liftOver preLift.bed hg19ToHg38.over.chain.gz conversions.bed unMapped
-
```

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.

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?

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?