I am working on gene coordinate conversion. I have a list of locations in the human genome, and I want to convert them in the chimp genome. Is there anyone who knows how to keep the input bed file in my output file? Thanks
Check here, maybe this help you!
When using liftOver, one approach is to do liftOver in both directions, i.e., from species A to B, and then back from the liftOver result from B back to species A:
A -> B -> A'
Then use bedmap or similar to get those intervals from A that are also found in A'.
This gives a conservative list of intervals preserved in a liftOver in both directions. Then you would go back to the A -> B step and filter B based on what was preserved between A <-> A'.
A -> B
A <-> A'
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