how to extract Granges not overlapping with other ganges?
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 21 months ago
India

Hi

  i Have two granges (gr1 and gr2) and i want to extract granges from gr2 that are not overlapping with  gr1. Please tell me the possible way to do it

Granges findoverlaps • 2.8k views
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Note that you already asked this 5 weeks ago here Non overlapping granges (or opposite of subsetByOverlaps) and got the same answer.

H.

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@james-w-macdonald-5106
Last seen 1 day ago
United States
> gr1 <- GRanges("chr1", IRanges(c(1,3,5), c(8,9,15)))
> gr2 <- GRanges("chr1", IRanges(c(1,3,5,17), c(8,9,17,35)))
> gr2[!gr2 %over% gr1,]
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [17, 35]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
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Also can use %outside% here instead of negating %over%.

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