Question: ChIP-seq differential binding analysis tools
gravatar for Jingyue
14 months ago by
United States
Jingyue30 wrote:

Hello all,

Do you recommend to overlap two or more differential peak calling tools to get a more stringent/accurate differential peaks?

Thank you!

chip-seq diffbind csaw • 291 views
ADD COMMENTlink written 14 months ago by Jingyue30

I do not see why you would want to do that. It only makes things more complicated. If you want to be more stringent better lower the FDR cutoff from like 10% to 5 or 1% or test against a certain fold change, e.g. 1.5, using glmTreat in csaw (the actual function comes from edgeR). Combining different tools is tricky as one would need to ensure that normalization, filtering etc. is more or less identical to have a meaningful analysis.

ADD REPLYlink written 14 months ago by ATpoint42k
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