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How are people handling biological replicates in ChIP-Seq experiments?
I recognize the benefit of analyzing replicates independently, but what is the "best" way to then combine this data and end up with a single list of bound regions/peaks? As peak calls tend to vary by a few bases, a simple intersect of the data doesn't seem to be the best idea.
However, combining the data pre-analysis concerns me also, as there is the (unlikely) possibility of a "strong" false peak in one dataset that may make its way through the analysis despite the fact that it doesn't exist in the replicate dataset...
Hope that's clear -- if not, I'm happy to attempt to clarify my situation.
Thanks!
(In case it's not painfully obvious from my post, I am NOT a bioinformatician or programmer in any way...."just" a biologist who's not afraid of the command line. BTW, this site a great resource -- I've read nearly everything on this site and may have even understood some of it.)
I recognize the benefit of analyzing replicates independently, but what is the "best" way to then combine this data and end up with a single list of bound regions/peaks? As peak calls tend to vary by a few bases, a simple intersect of the data doesn't seem to be the best idea.
However, combining the data pre-analysis concerns me also, as there is the (unlikely) possibility of a "strong" false peak in one dataset that may make its way through the analysis despite the fact that it doesn't exist in the replicate dataset...
Hope that's clear -- if not, I'm happy to attempt to clarify my situation.
Thanks!
(In case it's not painfully obvious from my post, I am NOT a bioinformatician or programmer in any way...."just" a biologist who's not afraid of the command line. BTW, this site a great resource -- I've read nearly everything on this site and may have even understood some of it.)