Instructions for batch liftover

Question

[rtho]

I need to remap about 100,000 short (<100bp) sequences from one assembly build into a newer one (same species, and all sequences should have a single, identical match). I've used LiftOver in the past but I'm not very familiar with the procedure for running batch submissions on a remote server. Can anyone direct me to a simple set of instructions that will indicate the data needs, formats and commands? Thanks

Answer 1

[Pierre Lindenbaum]

download a chain file eg.: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/ and the executable liftover: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ and run from a command line.