Question: Running featureCounts() in 'IntersectionStrict' mode
gravatar for Jon Manning
3.5 years 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 3.4 years ago • written 3.5 years ago by Jon Manning90
Answer: Running featureCounts() in 'IntersectionStrict' mode
gravatar for Wei Shi
3.5 years ago by
Wei Shi3.2k
Wei Shi3.2k 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 3.5 years ago by Wei Shi3.2k

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 3.4 years ago by Jon Manning90
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 227 users visited in the last hour