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Old 04-07-2009, 11:18 AM   #2
apfejes
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Location: Oakland, California

Join Date: Feb 2008
Posts: 236
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I would think this would depend on the aligner you're using, and what you plan to do with multi-match reads.

Depending on what you've precipitated in your ChIP, You're probably more interested in unique regions, anyhow, so I don't think it will make a big difference for the most part. If you were working with whole genome or wtss, I would expect it to have a bigger impact.
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