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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?

  1. Cusanovich, D. A. et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015).
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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

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