Question: Running featureCounts() in 'IntersectionStrict' mode
gravatar for Jon Manning
23 months ago by
Jon Manning90
Jon Manning90 wrote:

Hi all,

I'm counting reads to features, using featureCounts() via Rsubread, which is very nice, and fast- thank you.

For a particular application I need my variable-length, single-ended reads to fall entirely within the features, as in the IntersectionStrict mode of summarizeOverlaps() et al. Is there a way of making featureCounts() function in this manner? 

Many thanks,



ADD COMMENTlink modified 23 months ago • written 23 months ago by Jon Manning90
gravatar for Wei Shi
23 months ago by
Wei Shi2.8k
Wei Shi2.8k wrote:

Hi Jon,

No, featureCounts currently does not support this. When counting reads, featureCounts counts the number of bases in a read that overlap with a feature (the minOverlap parameter can be used to specify how many overlapping bases are required to assign a read to a feature, but this does not do exactly what you want to do) and we will extend this to check if bases in a read all fall within the feature. 

This new feature should be added to featureCounts fairly soon.

Best wishes,



ADD COMMENTlink written 23 months ago by Wei Shi2.8k

Thank you for the response. With this feature, and possibly the ability to use GenomicRanges objects rather than make SAF data frames, I'd never need to use the summarizeOverlaps.

ADD REPLYlink written 23 months ago by Jon Manning90
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