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Thank you for your answer !
Thank you @yfarjoun and @shlee. I did not know that Markduplicates did not count optical duplicates for single-end data on purpose. I thought there was a problem. I needed it because my team has aquired a new sequencer (Hiseq4000). Previously, we w…
Actually, you are right. I just realized after I wrote it. Indeed, with my single-end data, I did find duplicates. But Markduplicates never found any optical duplicates! I tried with many samples in many datasets (and by testing several values of op…
Thank you very much for your answer and for the information you gave me about secondary alignments. Actually, I think I understood what my problem was. I used single-end data (most of the projects in my team are single-end) and I just noticed Markd…
Thank you for this tutorial. Even if it is very clear, I met some problems. Could you help me ? I tried to use Markduplicates, following your tutorial, to estimate the number of duplicates due to the sequencer. I worked with a RNAseq 50bp single-end…