[BioC] Rsamtools - summarizeOverlaps - count read on complementary strand

[samuel collombet [guest]]

Hi!
I have RNAseq data which are single-end (50b), strand specific, but reads are the complement of the RNA (ie reads are always on the complementary strand to their corresponding gene). 
I would like to count reads on genes using summarizeOverlaps, however I do not find the way to tell him to count reads that are on the complementary strand to the exons. Is there a way? (with HTseq-count, I was using the option --stranded=reverse).

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