Dfference between intersectBed and multiIntersectBed

Question

[GouthamAtla]

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|    43585    43665    1    1    1    0
gi|589289284|ref|NW_006711693.1|    43585    43665    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 are the same, I do not understand why multiIntersectBed showing them in two separate lines ? I could not figure out the problem here.

[GouthamAtla]

It works after sorting both the files again. But I do not understand how the intersectBed is working without sorting.

[Aaronquinlan]

The intersect tool has alternate, tree-based method for finding intersections without sorting. It is slower and requires more memory, however.

[GouthamAtla]

That's interesting. Thanks.

Answer 1

[GouthamAtla]

Not to leave it as an open question, I'm answering it.

Intersectbed can also work without sorting the bed file. But multiintersectBed requires sorted bed file.