text: user8543: 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
  
  user8731: Check out the tool Intervene. It's exactly designed for this. Github link.
  
  user240: Venn diagrams can be helpful, but for peak calling they can be somewhat misleading.
  This topic is addressed in the DiffBind documentation, 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 (note, I have personally contributed to this tool in the past) and UpSet R packages are useful tools.
  
original_text: 8543: <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>
   8731: <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>
   240: <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>
  