Question: Visualising the number of overlapping peaks in ChIP-seq studies
1
gravatar for James Ashmore
2.6 years ago by
James Ashmore2.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.5k wrote:

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?

chip-seq • 2.2k views
ADD COMMENTlink written 2.6 years ago by James Ashmore2.5k
1

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.

ADD REPLYlink written 2.6 years ago by John12k

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

ADD REPLYlink written 2.6 years ago by geek_y8.7k

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

ADD REPLYlink written 2.6 years ago by Fidel1.8k

I have the same question as you have.

ADD REPLYlink written 2.4 years ago by Ming Tang2.4k

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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by steve1.7k
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