liftOver (convert BED files to another assembly)

[rebrendi]

Hello,

has anyone used the liftOver tool from UCSC Genome Browser in a command line? I downloaded the liftOver file and the corresponding .chain file, but it still does not work. It just says the command not found. I am using the following command line:

liftOver oldFile map.chain newFile unMapped

Any suggestions?
Thanks!

[Vasilisa]

Try .liftOver or ./liftOver, if this doesn't work, making liftOver executable (chmod +x) should help

[C.R.]

Yes, this is the correct way.
If you store the executable at a different place make sure that you provide the full path to it:

/pathToLiftover/liftOver oldFile /pathToLiftover/map.chain newFile unMapped

This should work, if you execute this from the folder were you placed the oldFile