Fraction of bases covered by each element in bed

Question

[avinash.sahu]

I am stuck in finding special kind of intersect of 2 bed files. I want to find for each entry of a.bed fraction (or number) of base-pairs overlapping at least one element of b.bed ( ignoring strand). b.bed itself can have overlapping entries. E.g.

a.bed

chr1    1       21      A
chr1    13      24      B

b.bed

chr1    4       11      +    1
chr1    6       12     -    2
chr1    7       15     -    3

output should be

chr1    1       20      A     11 (7+1+3)
chr1    13      24      B     2

Even if I can get unique overlap A those intersect one entry of B I can collapse them. However, bedtools-intersect reports non-unique overlap if b.bed entries are overlapping. Any solution?

Answer 1

[avinash.sahu]

CoverageBed of bedtools perform exactly that I was referring to. Sorry for the trivial question.