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Find unique non overlapping intervals between two files?

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
bed
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updated by harold.smith.tarheel harold.smith.tarheel • written by a.rex a.rex

1 answer

Use BEDtools subtract with -A option.

• 1 views • link
written by harold.smith.tarheel harold.smith.tarheel

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