0
$\begingroup$

I am using featureCounts from the subread package to count the number of fragments per gene in an RNA-seq experiment. I feed it a BAM file with paired-end reads aligned to a reference genome. In the help page of the executable, which I have installed using conda install subread, there is a section about overlaps, including for example the -O option which will assign the reads/fragments to all overlapping features. What is the default behaviour? Assigning to reads/fragments to the feature with largest overlap? not assigning multi-overlapping reads/fragments?

I would appreciate your help on this.

OS: macOS X

featureCounts version: 1.6.3

$\endgroup$
1
$\begingroup$

If a fragment overlaps multiple genomic features then it's unassignable, which is the appropriate way to handle ambiguous mappings when the resulting counts are then given to tools like DESeq2.

$\endgroup$
1
  • $\begingroup$ fair enough, so I will not use the -O option, thanks $\endgroup$ Mar 18 '19 at 10:44

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.