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Old 08-24-2010, 01:00 AM   #4
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

MeDIP-Seq is just another form of ChIP-Seq so in crude terms you can use the same techniques as you'd apply to ChIP-Seq to analyse MeDIP data. What I suspect you really want to know if if you should expect that the peaks you see in MeDIP should look like nice small independent events that many of the peak finders expect.

In our experience we see two kinds of enrichment in MeDIP data, there are small, highly enriched events which are very easy to identify and then there are slightly more diffuse, lower enrichment events which can be harder to pick out. The majority of reads will sit in the highly enriched peaks, and looking at these is a good place to start, but there may be some value in looking at the lower levels of enrichment.
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