How to keep the input bed coordinates of a bed?

Question

[yunzhe.jiang97]

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

[brunobsouzaa]

Check here, maybe this help you!

[Alex Reynolds]

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'.