I am looking to perform some motif identification in homer on sets of differential peaks that have been identified using edgeR and deseq2. I have peaks ranging in size from a few hundred base pairs to a few thousand base pairs. I did not explicitly set any parameters on the sizes of differential peaks to identify. From what I understand, it is not entirely sensible to perform motif identification using the full set of differential peaks. Instead, it is my understanding that it is more reasonable to either utilize the summits or to try and identify nfrs within the peaks and use those data for motif identification. Knowing that the performed ChIP was for H3K27ac, is it incorrect to proceed with the entirety of the differential peak set for motif finding?
if this is case, as I believe it to be, could anyone suggest a good method for isolating the regions to use for motif identification? I did much of my differential analysis using diff bind, so I know I can go back and set a summit parameter such that the identified differential peaks are of the denoted size. Additionally, I know that Diffbind3 now normalizes all differential peaks to 401 bps. I would imagine this may still be too large however...
Any information regarding best practices from performing motif identification on differential peaks obtained from H3K27ac data would be greatly appreciated!