I have a very specific question for the
-fraction option of the
featureCounts tool. I am analyzing single-cell data and only focusing on unique mapping reads. What I am aiming is that to weigh the counts for reads if they map to two different annotations that have an overlap.
So for example imagine a read gets mapped to two different annotations that have an overlap, then the total count for that read should be 1 (0.5 each) not 2 - is this what the
-fraction option does?
Or is there a better solution for this?
Another thing about the
-fraction is that it should be used with the -M (for multi-mapping reads) - while I have only allowed for unique mapping reads in my mapping step using
STAR - can this cause a problem?
Thank you for your inputs in advance.