Hello! I need to filter peaks which are withwin gene regions. I have .bam file from CHIP-seq experiment and .bam file from RNA-seq. I am trying to do this with this command:
bedtools intersect -a A.bam -b B.bam > AB.bam
The problem is that the output AB.bam is exactly the same as A.bam (it is visuable in IGV). Can someone give some advices?