Answers.Body: <p>Check out the tool <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1708-7" rel="nofollow noreferrer"><code>Intervene</code></a>. It's exactly designed for this. <a href="https://github.com/asntech/intervene" rel="nofollow noreferrer">Github link</a>.</p>
  
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Answers.CreationDate: 2020-05-27T22:25:32.593Z
Answers.Text: Dear @Cat if you describe Intervene for those of us who are unfamiliar with it?
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-04-27T17:28:53.647Z
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Answers.Body: <p>Venn diagrams can be helpful, but for peak calling they can be somewhat misleading.
  This topic is addressed in the <a href="https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf" rel="nofollow noreferrer">DiffBind documentation</a>, in the "Comparison of occupancy and affinity based analyses" section.</p>
  
  <p>Suffice to say, asking "which peaks are shared?" is not the same as asking "is there evidence for differential peaks, and where are they?".
  For this reason, performing a differential binding analysis might be a better option.</p>
  
  <p>If you're just looking for Venn diagram plotting software, though, the <a href="https://cran.r-project.org/web/packages/VennDiagram/index.html" rel="nofollow noreferrer">VennDiagram</a> (note, I have personally contributed to this tool in the past) and <a href="https://cran.r-project.org/web/packages/UpSetR/vignettes/attribute.plots.html" rel="nofollow noreferrer">UpSet</a> R packages are useful tools.</p>
  
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Answers.UserDisplayName: James Hawley
Body: <p>I have two outputs of macs2 peak calling for two of my data sets. I wanted to plot the Venn diagram to see how many peaks are shared. I mainly work on Unix/Linux. Do you know any way that I can have those diagrams plotted?</p>
  
  <p>Much Appreciated</p>
  
Tags: <phylogenetics><sequence-analysis><chip-seq><peak-calling><macs2>
Title: How to make Venn diagram for the Macs peak calling output of two data sets?
ThreadText: # How to make Venn diagram for the Macs peak calling output of two data sets?
  
  (Asked by: username_0 on 2020-04-27)
  
  I have two outputs of macs2 peak calling for two of my data sets. I wanted to plot the Venn diagram to see how many peaks are shared. I mainly work on Unix/Linux. Do you know any way that I can have those diagrams plotted?
  
  Much Appreciated
  
  **Tags:** phylogenetics, sequence-analysis, chip-seq, peak-calling, macs2
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2020-04-27. Score: 1
  
  Check out the tool [`Intervene`](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1708-7). It's exactly designed for this. [Github link](https://github.com/asntech/intervene).
  
  > **Comments:**
  > **username_2**: Dear @Cat if you describe Intervene for those of us who are unfamiliar with it?  
  
  ---
  
  ### Answer by username_3 on 2020-05-27. Score: 1
  
  Venn diagrams can be helpful, but for peak calling they can be somewhat misleading.
  This topic is addressed in the [DiffBind documentation](https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf), in the "Comparison of occupancy and affinity based analyses" section.
  
  Suffice to say, asking "which peaks are shared?" is not the same as asking "is there evidence for differential peaks, and where are they?".
  For this reason, performing a differential binding analysis might be a better option.
  
  If you're just looking for Venn diagram plotting software, though, the [VennDiagram](https://cran.r-project.org/web/packages/VennDiagram/index.html) (note, I have personally contributed to this tool in the past) and [UpSet](https://cran.r-project.org/web/packages/UpSetR/vignettes/attribute.plots.html) R packages are useful tools.
  
  
  ---
  
  