When I compare the two bed files using intersectBed and multiIntersectBEd, I see different results like:
multiIntersectBed -i R1_merge.bg R2_merge.bg | grep "gi|589289284|ref|NW_006711693.1|"
gi|589289284|ref|NW_006711693.1| 4358543665 1 1 1 0 gi|589289284|ref|NW_006711693.1| 4358543665 1 2 0 1
intersectBed -a R1_merge.bg -b R2_merge.bg | grep "gi|589289284|ref|NW_006711693.1|"
gi|589289284|ref|NW_006711693.1| 43585 43665
From multiIntersectBed, I am expecting something like:
gi|589289284|ref|NW_006711693.1| 43585 43665 2 1,2 1 1
Though the coordinates marked in yellow are same, I do not understand why multiIntersectBed showing them in two separate lines ? I could not figure out the problem here.