I have a question about enabling the fractions button in FeatureCounts. The subtext seems to contain a contradiction, because it states that the ‘NH’ value ( multimapped[MM] reads) will be used for the fractions (see image) of multimapped and overlapping reads. It does not say anything about how the overlapping genes are included in the fraction counts.
On the biostars forum (the --fraction option of featureCounts) it is explained that the MM reads are calculated by using the NH and the overlapping reads calculated by a separate variable ( which is missing from Galaxy:FeatureCounts)
My question: Is the NH value the only variable used for the calculation of fractional counts on Galaxy?