Hello,

I have a question relative to the featureCounts function, from the Rsubread package:

from the documentation:

"minOverlap: integer giving the minimum number of overlapped bases required for assigning a read to a feature (or a meta-feature). For assignment of read pairs (fragments), numbers of overlapping bases from each read in the same pair will be summed. If a negative value is provided, the read will be extended from both ends. 1 by default."

Does it mean that using a negative value, both reads from a pair should entirely overlap a feature to be counted ?

Thanks in advance !

No, the read pair will be counted as long as one of the two reads overlaps the feature by 1bp or more.