Intersectbed: Return Reads In Fraction In Input Files

Question

[anneleen.beckers]

I have a question with respect to intersectBED and multiple input files:

Is it possible to return reads which are present in, say 8/10 input files, without fractioning the reads in smaller intervals?

Thank you

Answer 1

[Alex Reynolds]

The BEDOPS suite includes bedops, a utility which performs various set operations on BED inputs. It's not clear if this would solve your specific problem, but you can specify the degree of overlap as criteria for inclusion, when using the --element-of operator with bedops.

For example, the following command would return elements from Reads.bed which overlap elements in Map.bed by 80% or more of segment length:

$ bedops --element-of -80% Reads.bed Map.bed