Answers.Body: <p>I would agree with your statement.  Typically the ratio of unique to duplicated reads is a function of input library complexity (number of input molecules) verse sequencing depth (the amount of molecules sequenced).  </p>
  
  <p>In the example you gave you have about a 2:1 ratio of duplicates to unique reads which suggests that these libraries have been sequenced to their fullest and additional sequencing would yield few new unique reads.</p>
  
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Answers.Text: The higher number of duplicates could be in a high-complexity library sequenced very deep or in a low-complexity library sequenced with many fewer reads. Without more info from OP it is hard to interpret.
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Answers.Text: the x-axis provides the total number of reads.  either way it is the ratio that is important to tell you if the sequencing has saturated the library.
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Body: <p><a href="https://i.sstatic.net/sv8xr.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/sv8xr.png" alt="enter image description here"></a></p>
  
  <p>FastQC of my sample files, aggregated into a single plot by MultiQC. Blue represents unique reads. Black represents duplicate reads. The x-axis is the number of reads.</p>
  
  <p>I see I have more duplicate reads than unique reads, how do I interpret this plot? This is my attempt:</p>
  
  <blockquote>
    <p>FastQC took the first 100,000 sequences in each sample (<a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/8%20Duplicate%20Sequences.html" rel="nofollow noreferrer">details</a>).
    Generally, higher duplicated read percentage is welcome as it
    represents better sequencing depth and lower sequencing error
    contamination. This dsitribution in this plot looks reasonable and
    nothing unusual.</p>
  </blockquote>
  
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Comments.CreationDate: 2018-10-25T02:55:27.130Z
Comments.Text: Can you provide us with some more info, including the typical number of reads in each library, the library type, source material, et cetera? It's hard to tell how to interpret your data without that info. If it's single-cell versus a sample from bulk tissue that makes a big difference in complexity. Also, something like RNA seq will have more duplicates that genome sequencing library types.
Comments.UserDisplayName: conchoecia
Tags: <fastqc>
Title: How to interpret duplication from MultiQC/FastQC?
ThreadText: # How to interpret duplication from MultiQC/FastQC?
  
  (Asked by: username_0 on 2018-10-25)
  
  [![enter image description here](https://i.sstatic.net/sv8xr.png)](https://i.sstatic.net/sv8xr.png)
  
  FastQC of my sample files, aggregated into a single plot by MultiQC. Blue represents unique reads. Black represents duplicate reads. The x-axis is the number of reads.
  
  I see I have more duplicate reads than unique reads, how do I interpret this plot? This is my attempt:
  
  > FastQC took the first 100,000 sequences in each sample ([details](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/8%20Duplicate%20Sequences.html)).
  > Generally, higher duplicated read percentage is welcome as it
  > represents better sequencing depth and lower sequencing error
  > contamination. This dsitribution in this plot looks reasonable and
  > nothing unusual.
  
  **Tags:** fastqc
  
  > **Comments:**
  > **username_1**: Can you provide us with some more info, including the typical number of reads in each library, the library type, source material, et cetera? It's hard to tell how to interpret your data without that info. If it's single-cell versus a sample from bulk tissue that makes a big difference in complexity. Also, something like RNA seq will have more duplicates that genome sequencing library types.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-10-25. Score: 0 | Accepted answer
  
  I would agree with your statement. Typically the ratio of unique to duplicated reads is a function of input library complexity (number of input molecules) verse sequencing depth (the amount of molecules sequenced).
  
  In the example you gave you have about a 2:1 ratio of duplicates to unique reads which suggests that these libraries have been sequenced to their fullest and additional sequencing would yield few new unique reads.
  
  > **Comments:**
  > **username_1**: The higher number of duplicates could be in a high-complexity library sequenced very deep or in a low-complexity library sequenced with many fewer reads. Without more info from OP it is hard to interpret.  
  > **username_2**: the x-axis provides the total number of reads.  either way it is the ratio that is important to tell you if the sequencing has saturated the library.  
  
  ---
  
  