I just wonder if you guys have some thoughts on this?
I have run with MarkDuplicates, but maybe I should also spend some time running it again without marking of duplicates..
We currently don't have any recommendations for RNAseq, sorry. We've started a project to look into it but it's still early days; it'll probably be a few months before we have anything ready to share with the public.
I have quite a few mRNAseq projects in near future, so thats good news!
Looking forward to that.