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How to keep the input bed coordinates of a bed?

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
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written by yunzhe.jiang97 • yunzhe.jiang97

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'.

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written by Alex Reynolds Alex Reynolds

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