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.
Dear Carlo thank you for your input - I do use featureCounts from the
subread/2.0.0package. So based on what you have mentioned, then
-Oseems what I want. But the question is
-Oalso weighs the counts for overlapping features if only unique mapping reads are considered (I excluded all the multi-mapping reads and working only with unique mapping reads)?
Yes yes, it is not a problem. A read can be uniquely mapped (one genomic position) but overlap multiple features.
great help - thank you so much :)