The name for the option that controls whether reads mapping to multiple features are counted or discarded is poorly chosen:
counting:
count_nonunique: TRUE # boolean (see inter.feature argument of summarizeOverlaps)
count_nonunique (default = TRUE) is directly passed to inter.feature of summarizeOverlaps, which says:
A logical indicating if the counting mode should be aware of overlapping features. When TRUE (default), reads mapping to multiple features are dropped (i.e., not counted). When FALSE, these reads are retained and a count is assigned to each feature they map to.
The name _countnonunique implies that nonunique reads are counted if TRUE and not counted if FALSE, however the summarizeOverlaps inter.feature option uses the reverse sematic logic. Therefore this name in the settings should be changed (or clearly annotated) to indicate which effect it has.
The name for the option that controls whether reads mapping to multiple features are counted or discarded is poorly chosen:
count_nonunique (default = TRUE) is directly passed to inter.feature of summarizeOverlaps, which says:
The name _countnonunique implies that nonunique reads are counted if TRUE and not counted if FALSE, however the summarizeOverlaps inter.feature option uses the reverse sematic logic. Therefore this name in the settings should be changed (or clearly annotated) to indicate which effect it has.