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?
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.
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.
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.