single-end data and optical duplicates (Mark Duplicates)
I met a problem with MarkDuplicates: I tried to estimate optical duplicates with both single-end and paired end datasets.
In both cases, MarkDuplicates was able to detect duplicates and to mark them. However, in single-end datasets, it always says to me "Found 0 optical duplicate clusters" (I tested with several samples and several datasets -- I cannot believe there is 0 optical duplicates in all these samples). I tried Markduplicates in only 2 paired-end samples and each time it could detect optical duplicates (12% and 6% of optical duplicates among duplicates).
I really do not understand these results. Is there something I missed, like a parameter, or something?
For information, my data were sequenced on the Hiseq4000 and I followed this tutorial: http://gatkforums.broadinstitute.org/gatk/discussion/6747/how-to-mark-duplicates-with-markduplicates-or-markduplicateswithmatecigar
Thank you very much!