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Merge/Collapse regions within a certain distance

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
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Adrian Pelin Adrian Pelin

1 answer

bedtools merge with option -d

-d  Maximum distance between features allowed for features
    to be merged.
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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Adrian Pelin Adrian Pelin

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?

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written by Adrian Pelin Adrian Pelin

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