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.