Excluding intervals with repeats

Question

[rbronste]

Is there a quick and easy method for excluding intervals from a bed file that contain any kind of repetitive elements? Thanks.

Answer 1

[ATpoint]

Given that you have a file with the repeats in BED format, you may use BEDtools intersect with the -v option:

bedtools intersect -v -a your.bed -b repeat.bed > your_without_repeats.bed

[rbronste]

Yes I was thinking of doing it this way, one weird thing though is if I do:

bedtools intersect -v -a your.bed -b repeat.bed > your_without_repeats.bed

Lets say I get 300 out of an original 1000 for:

your_without_repeats.bed

However when I do the following to get a file of those intervals that overlap with repeats:

bedtools intersect -a your.bed -b repeat.bed > your_with_repeats.bed

I don't get exactly 700, but another number?

[ATpoint]

The reason for this is that the second command outputs parts of an -a that partly overlap b. In that case the non-overlapping part of the interval is outputted. If you use -wa option, you should get 700.