Hi, I have a question about the definition of consensus peak set. I can think of two options:
A) One single peak set from adding and merging multiple peak sets. akin to: cat 1.bed 2.bed | bedtools merge -stdin > consensus.bed
B) A "pooled" peak set consisting of all the peaks from the two input peak sets. akin to: cat 1.bed 2.bed > consensus.bed
Which one is it?
The reason I ask is because I am trying to decide whether it would be a good idea to perform IDR on my samples and use the single IDR-cutoff peak set as the "consensus" for differential binding analysis. I would do this if A) is the right answer. However, if it is B) then IDR is somewhat redundant, as diffbind would just tell me all of the peaks that are significant.
Thanks in advance.