I have divided genomic regions from human and mouse into 200bp windows. I wanted regions in Human/Mouse that are present as one to one mapping in other species is there a quick way to get the one to one mapping for each region rather than running liftover again over all these regions one at a time and checking if these regions have a single mapping or many mappings or no mapping across the two assemblies?
So what I am trying to do here is get regions that can be liftOvered to another species. So for example I have three files human coordinates (200bp windows), and Mouse coordinates (200 bp windows) the output I expect is a file HstoMm and vice versa for MmtoHs.
I have tried to run liftover for each position in parallel to do that since I don't know of any other way to do it. But running liftover for each position in parallel for a single chromosome is taking a long time and is nowhere close to be done after running for 1 day. I was wondering if there is a smarter and quicker way to do it.