How to keep the input bed coordinates of a bed?
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12 months ago

Hi,

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

bed liftOver • 291 views
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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'.