Visualising the number of overlapping peaks in ChIP-seq studies

Question

[James Ashmore]

I am usually asked if I can show the overlap between peaks in ChIP-seq studies using a venn diagram. However a venn diagram supposes the relationship is 1:1, where as a single peak in one sample could overlap multiple peaks in another sample. My question is how do you normally calculate the amount of peak overlap and how do you prefer to visualise/summarise this overlap?

[John]

This is a common misconception that even the most seasoned analysts make.
A peak isn't a single entity. Its a region of the genome. You shouldn't use Venn Diagrams (or any other categorical visualization) for something with a beginning, end, and ideally intensity. Check out the deeptools package to see how to overlay positional information for 1 or more categories of sample/feature.

[GouthamAtla]

Software To Find Overlaps Of Chip-Seq Peaks In Multiple Samples.

[Fidel]

I haven't tried myself but venneuler for R seems like what you need: http://ieeexplore.ieee.org/xpls/icp.jsp?arnumber=5728808&tag=1

[Ming Tommy Tang]

I have the same question as you have.

[steve]

I have a post here about how to do this with mergePeaks in HOMER and the VennDiagram package in R, and also a post here about how to do the same with UpSet plots.