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Old 12-06-2012, 06:52 AM   #3
Location: U.S.

Join Date: Oct 2012
Posts: 17

Thanks for your helpful response. I had looked into DESeq, but it also didn't return what I expected (and also doesn't handle multi-mapping reads, which I have a lot of). I have been thinking our data may be more variable than we can work with, so I'm looking into mask files and this sort of thing, but I'm wondering - is there a standard metric(s) for reporting variability? I'm pretty new at this, and wondering, generally, how I might decide whether or not my samples are usable for this kind of analysis.
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