I am using “Multiple Intersect function” to identify # of regions overlapping amongst three different ChIP-seq narrow Peaks regions.
When I get the results for “multiple Intersect function”, the Total # of regions for each ChIP-seq are different from my input file. There are more regions than there were originally for all three data files.
For example, one of the three files had 63,251 regions, but “mutliple intersect function” results suggest that there are 105,417 regions. This is the number I counted all the "1"s for my file. Am I doing something wrong?