Hello Everyone,

I have results from two ChipSeq experiments.  

Experiment A has 1900 peaks and Experiment B has 4000 peaks.

When I create Venn Diagram using the interval data, the total number of resulting regions numbers almost 10000.  This is much higher than the sum of the two groups.

This occurs because certain interval from the two Experiments are being split.  

So if interval 1 is 10-100 and interval 2 is 50-150, this results in 3 separate genomic regions  (0-50 (A only), 50-100 (A and B), and 100-150 (B only)).

Is there a way to control this behavior. For instance, I do not want these intervals to be split into three, but treated as one.  So even if there is only one base pair overlap, it should be called A and B.  

Otherwise, 5900 peaks end up in 10,000 genomic regions which is hard to explain to biologists.

Any help is appreciated on this matter.

Vivek

Hi Vivek,

It has been a while since I looked at the interval or VennDiagram code, so I am not sure exactly what you are trying to do and the steps you are using to do it. 
It sounds like you want to join the two intervals A and B together to create the 'A and B' interval using the IntersectOutputType::OverlappingIntervals rather than the OverlappingPiecesOfIntervals modifier for the SequenceRangeGrouping in the CreateSequenceRangeGroupingForVennDiagram in VennToNodeXL.cs.

If you are writing C# and using the library to produce the Venn diagram, you might be able to clone a bit of the code into your source and set the IntersetOutputType for what you want to do.  If you are doing it in excel, the plug-in and/or the library will have to be modified.

If you have a set of small sample files and the steps you are taking, we could arrange some discuss what you want to and how to do it.

-bobd-