Running featureCounts() in 'IntersectionStrict' mode
1
0
Entering edit mode
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
ADD COMMENT
2
Entering edit mode
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

 

ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 264 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6