**5.3k**wrote:

Apologies if this is blatantly obvious!

I would like to compare coordinates in setA with those of setB.
The output should have the same number of coordinates as setA and tell me how many nucleotides of each setA coordinate are overlapped by **any** coordinate in setB.

For example a large coordinate in setA may be overlapped by two setB coordinates, but i want to know how many nucleotides of the setA coordinate are covered by both setB coordinate in total.

I know how to do this on GALAXY as there is the handy 'Coverage' tool in 'Operate on Genomic Intervals'. However, i want to do this on the command line. I have been trying to get BEDTools to do this using 'intersectBed', but i can only seem to get just the overlapping setA coords (using -u), or get the nucleotide over for multiple setB coordinates on separate line (using -wao), or a count of how many setB overlaps setA (using -c).

SetB coordinates are non-overlapping themselves, so i guess i could tally up those SetB coordinates that overlap the same setA coordinate.

Can BEDTools do what i want or there another command line way of doing what i want?

Thank you!

PS I have also sent the to BEDTools discussion, so apologies for any double postings!