I am always confused whether we should resize peak before ATAC/ChIP-Seq differential peak analysis (DA). I have see some DA tools or DA review or paper. Some use the resize while some do not. But it seems that it do not say the advantages and disadvantages. Now I am using DiffBind to DA. It recommend resize peak when dealing with broad peak, like H3K27me3.
For me, I think we should not resize the peak, after all, we do not resize gene when do RNA DA. But if we do not resize, it will introduce a lot of noise when dealing with motif analysis.
So I am wondering whether some one can give me addvices.