the --fraction option of featureCounts

1

Hi all,

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.


RNA-Seq


featureCounts


rna-seq


genome


sequencing

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