Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-23T17:01:51.810Z
Answers.LastActivityDate: 2018-07-23T17:01:51.810Z
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Body: <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>
  
Tags: <single-cell><atac-seq><pcr><duplications>
Title: How is PCR duplication rate computed in scATAC-seq?
ThreadText: # 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
  
  
  ---
  
  ## 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
  
  
  ---
  
  