<p>The answer is in the <a href="http://science.sciencemag.org/content/sci/suppl/2015/05/06/science.aab1601.DC1/Cusanovich-SM.pdf" rel="nofollow noreferrer">supplementary methods page 3</a>.</p>

<blockquote>
  <p>Finally, all fragments in the same library with duplicate start and
  end coordinates were removed using Picard</p>
</blockquote>

CC BY-SA 4.0
2018-07-23T17:01:51.810Z
2018-07-23T17:01:51.810Z
GWW
<p>Reading Cusanovich et al. (2015) I encountered the sentence:</p>

<blockquote>
  <p>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).</p>
</blockquote>

<p>How is PCR duplication rate computed?</p>

<ol>
<li>Cusanovich, D. A. et al. <a href="http://science.sciencemag.org/content/348/6237/910" rel="nofollow noreferrer">Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing.</a> Science 348, 910–914 (2015).</li>
</ol>

<single-cell><atac-seq><pcr><duplications>
How is PCR duplication rate computed in scATAC-seq?
# How is PCR duplication rate computed in scATAC-seq?

(Asked by: username_0 on 2018-07-23)

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.](http://science.sciencemag.org/content/348/6237/910) Science 348, 910–914 (2015).

**Tags:** single-cell, atac-seq, pcr, duplications

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## 1 answers

### Answer by username_1 on 2018-07-23. Score: 3 | Accepted answer

The answer is in the [supplementary methods page 3](http://science.sciencemag.org/content/sci/suppl/2015/05/06/science.aab1601.DC1/Cusanovich-SM.pdf).

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


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