bedtools Multiple Intersect

[srinivasa_abishek]

Hi there,

The Multiple intersect tool gives the common intervals between bed files with at least 1 nucleotide overlap. Is there a tool that gives the common intervals between (atleast 3) bed files that are not overlapping but 1000bp in distance?

Abishek

[wm75]

Don’t know such a tool, but I also don’t have an easy time imagining one. So with multiple files, what’s your definition of 1000bp apart. Where’s the anchor point for that? Or would you allow chaining of features?