Running featureCounts() in 'IntersectionStrict' mode
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Jon Manning ▴ 90
@jon-manning-5708
Last seen 5.1 years ago

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,

Jon

rsubread featurecounts summarizeoverlaps • 898 views
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Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 1 day ago
Australia/Melbourne/Olivia Newton-John …

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,

Wei

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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.