How is PCR duplication rate computed in scATAC-seq? Reading Cusanovich et al. (2015) I encountered the sentence:


  We mixed pairs of cell lines (HEK293T or HL-60 versus GM12878), performed combinatorial cellular indexing, and sequenced the resulting libraries to saturation (65% duplicate rate).


How is PCR duplication rate computed?


Cusanovich, D. A. et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015).
The answer is in the supplementary methods page 3.


  Finally, all fragments in the same library with duplicate start and
  end coordinates were removed using Picard