Hi,
Thanks for the response. I tried the following:
bedtools intersect -a N_optimal.bed -b optimal_merged.bed > test.bed
N_optimal.bed = optimal peak list for one cell type
optimal_merged.bed = global peak list for all three cell types combined
However, when I do this, test.bed comes out exactly the same as N_optimal.bed (which I would expect as all of the peaks in N_optimal.bed will overlap with peaks in optimal_merged.bed). I am a bit confused as to how I can use this to get the summits for the global peak list.
Best wishes,
Lucy