Hi all, I'm curious what people are using these days for finding peaks in MeDIP-seq data (I have two experimental conditions, each with replicates, and I'm interested in finding changes between them). I've browsed through a number of common tools, such as MACs, but they seem to suggest pooling biological replicates into a single .bed file for further analysis. I would assume that it's beneficial to exploit the presence of replicates for judging noise and am wondering if there's something else out there. Alternatively, if someone can point me to where this sort of issue is discussed in the MACs manual I'd appreciate it.
Alternatively, do people recommend using MACs or a similar tool to give a first pass at finding peaks, which can then be used as regions of interest for other tools (which I suppose I could just write, but I assume others have already done that).
Alternatively, do people recommend using MACs or a similar tool to give a first pass at finding peaks, which can then be used as regions of interest for other tools (which I suppose I could just write, but I assume others have already done that).
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