Sorry I should have added my reply here.
I considered that it doesn't take into account secondary alignments as none of them were flagged as duplicates (although I really have a lot of them). And I think I read it somewhere...
Thanks for the solution suggested, that's kind of what I thought doing. It's strange that I can do it in an easier way with largely used tools though.
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mathieu.bahin
First of all, why do you want to remove duplicate reads from RNA-seq data?
This is MeRIP data, I want to find info about methylated genes (and other features if so). After the mapping, I'll do peak calling. I think that duplicated reads will noise the results no?
Removing multimapped reads should be okay but I am skeptical about removing duplicates.
Indeed I'd prefer to use only the uniquely mapped reads but then I'd keep only 3% of my dataset...
Thanks for the link on how both of the tools work.
From what I understand, secondary alignments are not even considered by MarkDuplicates. So my guess is that if several secondary alignment reads are mapped to
chr1,10000,10100, they won't be marked as duplicate although they could be. So I don't see how I can work with MarkDuplicates as long as I decide to keep multimappers?I don't think programs marking duplicate reads considers whether they are primary alignment or secondary alignment. But I see your point that if primary aligned read is duplicate, then the secondary aligned reads also may be considered as duplicates. Quick alternative way I could think of is, mark the duplicate reads, get the read names of duplicate reads and then use that list to remove all the reads with same name. This way, removes all other alignments of a duplicate read.