I have 7 biological replicate of a normal sample after peak-calling I converted it into bed files and now I want to find what are the common region between those .
So i tried with bedtool intersect
my command is this bedtools intersect -a SRR2920506.filtered.bed -b SRR2920531.filtered.bed SRR2920466.filtered.bed SRR2920478.filtered.bed SRR2920507.filtered.bed SRR2920532.filtered.bed > answer.bed
it says " the intersect tool can detect overlaps between a single -a file and multiple -b files (instead of just one previously). One simply provides multiple -b files on the command line."
My doubt is the file that goes to "a" argument is not query which i have to detect overlaps against "b" files as these are all biological replicate. Am i doing the right way?
Secondly I tried with
bedops but the number of overlaps which is reported is really low when i compare the result which i get from bedtools intersect function.
Any suggestion or help regarding how to intersect multiple would be really appreciated