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Very simple question, whats the preferred method to remove peaks from analysis that are associated with single replicates only? Thanks.
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I'm sure there are a lot of ways to do it. In the past, I've just loaded the peak file into an R GRanges format and removed any peaks that didn't show any overlaps in findOverlaps(). You can change the parameters to find overlaps of certain lengths as well. But I don't actually know how kosher this is or if there other tools that would make this easier.
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