Question: Find unique non overlapping intervals between two files?
0
gravatar for a.rex
19 days ago by
a.rex170
a.rex170 wrote:

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 • 105 views
ADD COMMENTlink modified 19 days ago by harold.smith.tarheel4.2k • written 19 days ago by a.rex170

Try and explore bedtools intersect and bedops

ADD REPLYlink written 19 days ago by shenwei3564.2k
0
gravatar for harold.smith.tarheel
19 days ago by
United States
harold.smith.tarheel4.2k wrote:

Use BEDtools subtract with -A option.

ADD COMMENTlink modified 19 days ago • written 19 days ago by harold.smith.tarheel4.2k
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