Question

Merge/Collapse regions within a certain distance

0

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7.3 years ago

Adrian Pelin ★ 2.6k

Hello, I am sure this has been asked before but I can't find it. Basically:

scaffold_1 100 200
scaffold_1 300 400
scaffold_1 1000 2100

merge features at a minimum proximity of 200bp and:

scaffold_1 100 400
scaffold_1 1000 2100

Is this possible? Thanks, Adrian

bedtools • 1.3k views

ADD COMMENT • link updated 7.3 years ago by Pierre Lindenbaum 161k • written 7.3 years ago by Adrian Pelin ★ 2.6k

score 1 · Answer 1 · 2017-01-15

1

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7.3 years ago

Pierre Lindenbaum 161k

bedtools merge with option -d

-d  Maximum distance between features allowed for features
    to be merged.

ADD COMMENT • link 7.3 years ago by Pierre Lindenbaum 161k

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Did not realize that would work for only one file. Thanks!

ADD REPLY • link 7.3 years ago by Adrian Pelin ★ 2.6k

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Actually it seems like it takes only one file as input. This makes things complicated in certain cases. Is there any way to only merge features from file A to those of file B, but not merge features within file A or within B?

ADD REPLY • link 7.3 years ago by Adrian Pelin ★ 2.6k