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bedtools coverage double-counting

I am using bedtools coverage to calculate coverage at various regions, but I also want to know how many reads are overlapping any of the regions. Sometimes the regions are close, so the reads span more than one and those reads get counted twice. Is there any way to prevent that or maybe an alternate method that can do that?

bedtools
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updated by harold.smith.tarheel harold.smith.tarheel • written by igor igor

Have a look also at htseq-count, it has options to decide what to do with ambiguous overlaps. And also featureCounts (about which I have no experience though).

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written by dariober dariober

1 answer

You could use bedtools intersect with the -c flag to report the number of overlaps for each read, then change any values >1 to 1 and sum (or filter out the reads with zero overlap and count the number of unfiltered reads).

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written by harold.smith.tarheel harold.smith.tarheel

bedtools intersect -c seems a good strategy to first get reads overlapping one and only one feature (i.e. count = 1). Then you need covergeBed to actually count the (now unambiguous) reads in each feature.

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written by dariober dariober

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