Collapse bed and only sum overlapping parts
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Entering edit mode
7 months ago
Matthias ▴ 30

Hi,

I have a bed that looks something like this:

chr1    150000    170000    feature    10    +
chr1    160000    180000    feature    10    +

I want a way to sum the scores in only the overlapping regions, like this:

chr1    150000    160000    feature    10    +
chr1    160000    170000    feature    20    +
chr1    170000    180000    feature    10    +

Does anyone have any ideas how to do this? I wrote a super chunky python script, but its super computationally intensive and there must be a better way.

Thanks!

bed RNA-Seq alignment • 220 views
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Entering edit mode
7 months ago
Matthias ▴ 30

Figured out a bedops bedmap option:

bedops --partition my.bed |  bedmap --echo --sum --delim '\t' - my.bed

Input bed needs to be sorted first.

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