I have a sequencing dataset for which I want to remove the duplicates (PCR and optical). I aligned it with TopHat2 and STAR allowing a maximum of 5 locations for the multimappers.
I used MarkDuplicates to mark the duplicates but I happened to find that only primary alignments were marked (and I read that this is the expected behaviour).
Is there a reason why we can't mark seconday alignment reads? Is there an option to do that with MarkDuplicates that I would have missed? Otherwise, which tool can do that?