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?
Dear @PARKS98,
Just to clarify, becasue I am unsure what tool you have used. Was it bedtools Multiple Intersect? Please have a look at the example, for that tool, to see why you have more “regions” in your result file. The tool outputs subregions based on the intersections of your input files. That means, your original regions are probably split into mutliple regions in your result and thus you have more lines in the output than in the input.
Thanks for getting back to me. Yes, my question is on bedtools multiple interect. Maybe I am using this tool incorrectly, but what I did was-
Input – I input three different ChiP-seq MACS narrow peaks bed files because I was interested in their overlaps. ( I could have used Intersect, but I had three inputs instead of two).
Output – Yes, it seems like the output file gather all regions from three input files. My question was that when I counted all the “1”s for each input files, they were more than the original input files. I am sorry but I still don’t get how splitting into multiple regions give more results. Do you mean for instance one interval can be split into two or more during this bedtools multiple intersect?