How To Overlap Human And Mouse Genomic Regions (Ex: Chip-Seq Peaks)

Question

[biorepine]

Hi I am trying to overlap hg19 and mm9 genomic regions. Should I liftover hg19 to mm9 before I overlap ?

thanx

Answer 1

[Ido Tamir]

Obviously yes. And you might have to lower the "Minimum ratio of bases that must remap" in order to not loose too much, and do this in both directions (hg19 -> mm9, mm9 -> hg19, to check for consistency).

Oh, advice is so very cheap to give.

[biorepine]

Do you have any idea about optimal cutoff for the "Minimum ratio of bases that must remap". by default it is 0.95.