Hello,
I have reads that were sequenced using HiSeq X. I want to identify the number or percentage of optical duplicates in the reads.
The description in MarkDuplicates mentions that set the maximum offset between two duplicate clusters in order to consider them optical duplicates, for HiSeq X, should be set to ~2500. However, the maximum limit is 500. Is there a way to get optical duplicates for HiSeq X?