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

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

thanx

human mouse chip-seq
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updated by Ido Tamir Ido Tamir • written by biorepine biorepine

1 answer

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.

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written by Ido Tamir Ido Tamir

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

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written by biorepine biorepine

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