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Old 08-24-2010, 08:06 AM   #7
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

We do our analysis within SeqMonk (which we write, so we're somewhat biased!) rather than using an external peak caller.

Normally we'd use the contig based probe generator to do the cluster detection. This allows you to set an enrichment threshold and build clusters where your reads exceed this threshold. There are then facilities for merging adjacent peaks or rejecting enriched regions which are too short. We find that this kind of approach lends itself well to more unusual ChIP experiments where the shape of the peaks might not be what you'd expect from a traditional 'transcription factor' type enrichment.
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