SEQanswers - View Single Post - Masked or unmasked genome for ChIP-seq analysis?

apfejes · 04-07-2009, 11:18 AM

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.

04-07-2009, 11:18 AM	#2
apfejes Senior Member Location: Oakland, California Join Date: Feb 2008 Posts: 236	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. __________________ The more you know, the more you know you don't know. —Aristotle