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