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
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2 Answers
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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.
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Check out the tool Intervene. It's exactly designed for this. Github link.
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$\begingroup$ Dear @Cat if you describe Intervene for those of us who are unfamiliar with it? $\endgroup$– M__ ♦May 27, 2020 at 22:25