Query fo LiftOver

[Kumar, Yogesh]

Hi, 

I have downloaded liftover tool  to use as command prompt because my file size is very large and online website has limitation to upload the file to convert coordinates from one genome to another genome.

Could you advice me , how could i use liftover tool on command prompt? 

 How could i install liftOver tool on linux 

[Jairo Navarro Gonzalez]

Hello Kumar,

Thank you for using the UCSC Genome Browser and your inquiry.

After you download the liftOver utility, you can run the program by navigating to the directory with the liftOver executable and then calling the program. To call the program from any directory, you will have to add the directory containing the liftOver program to your PATH variable.

./liftOver

If you run the program without any arguments, you will see the usage statement. 

$ ./liftOver
liftOver - Move annotations from one assembly to another
usage:
   liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

When you first download the liftOver utility, you will have to make the binary file executable, i.e.:

chmod +x liftOver

You can also view our mailing-list archives for guidance if you run into any other issues. Pre-generated files are available for selected assemblies from the downloads page.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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