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