Question: How do I do a bedtools like intersection in GenomicRanges?

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endrebak85 •

**30**wrote:GenomicRanges intersect is more like what I would call set intersect - first the sets of A and B are computed, then intersection is done.

Bedtools intersect finds the intersect of each interval in A with each interval in B which means that in the worst case, the number of output regions is the size of the cartesian product of A B as in the example below:

$ cat A.bed chr1 10 32 chr1 30 40 $ cat B.bed chr1 15 35 $ bedtools intersect -a A.bed -b B.bed chr1 15 32 chr1 30 35

Is this type of intersect possible in genomicranges? Thanks.

Edit: fixed example

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modified 11 months ago
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Michael Lawrence ♦

**11k**• written 11 months ago by endrebak85 •**30**