Question

Venn diagram of peaks between three tissue types using DiffBind

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Divya • 0

@divya-24294

Last seen 3.3 years ago

Hello,

I'm new to DiffBind and have 3 tissues with 2 replicates each. I have been able to generate plots with contrast 1-3 to compare each pair. I'd like to plot a Venn diagram of the peaks in the 3 tissue types and unable to do so withour errors.

DiffBind • 648 views

ADD COMMENT • link updated 3.4 years ago by Rory Stark ★ 5.1k • written 3.4 years ago by Divya • 0

score 0 · Answer 1 · 2020-12-02

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Rory Stark ★ 5.1k

@rory-stark-5741

Last seen 7 days ago

Cambridge, UK

Can you supply a bit more detail on what you are trying to do? Perhaps the code that isn't working? Are you trying to overlap all the peaks, or peaks in either/both replicates, or differentially bound peaks?

ADD COMMENT • link 3.4 years ago Rory Stark ★ 5.1k

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I am trying to plot overlap of all peaks in the 3 tissue type. Tissue 1/2 and 3. When I try PlotVenn I get a venn with overlap of "1 vs 2", "1 vs 3" and "2 vs 3" instead of the overlap between tissue 1, 2 and 3 (accounting for 2 replicates)

ADD REPLY • link 3.4 years ago Divya • 0

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Are you looking for an overlap between the consensus of the replicates for each tissue type?

Can you share a code snippet? If I could see samples in your DBA object and your call to dba.plotVenn(), I could see what is going on.

ADD REPLY • link 3.4 years ago Rory Stark ★ 5.1k