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Old 11-03-2009, 01:49 PM   #1
nbr
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Location: Chicago

Join Date: Oct 2009
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Default Simulating random ChIP-seq peaks

Does anybody have a good way of generating random ChIP-seq peaks?
The goal is to generate random sets to assess statistical significance of overlap of real ChIP-seq peaks with different genomic features.

Simply generating random coordinates does not suffice because ChIP-seq peaks are biased for non-repetitive regions, and of course, only assembled regions of the genome, and possibly have some GC bias.

I wonder if simply excluding the repetitive and unassembled regions of the genomes would do a good job. Another possibility would be using huge amounts of input data, using mapped reads as "anchors" for randomly generated peaks?

Thanks!

Last edited by nbr; 11-03-2009 at 01:52 PM.
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