Find unique non overlapping intervals between two files?

Question

[a.rex]

I have two bed files, and I want to find unique non-overlapping intervals between the two files, given there is less than 30% overlap E.g

File 1: 

interval1   5248    6157
interval2   6200    6393
interval3   6800    7493
 ...

File 2: 

gene1   5258    6257
gene2   7800    7993
gene3   8900    8993
...

Unique to file 3: 

gene2   7800    7993
gene3   8900    8993

[shenwei356]

Try and explore bedtools intersect and bedops

Answer 1

[harold.smith.tarheel]

Use BEDtools subtract with -A option.