This is more of a conceptual question, so I hope it makes sense.
When I merge peaks between two files using Homer, Homer's page on merging peaks says "[i]t's default behavior is to take two or more peak files and return a single peak file containing the unique peak positions from the original files" (found here: http://homer.ucsd.edu/homer/ngs/mergePeaks.html).
So, I am picturing an example: let's say I have two peak files, a.peak.file and b.peak.file. Both a.peak.file and b.peak.file have ten peaks each, with five of those peaks being identical to each other. Does that mean that if I want to merge them into a new file, c.peak.file, that c.peak.file will only have 10 peaks?
That is to say, it is NOT additive. 10 peaks from a.peak.file + 10 peaks from b.peak.file = 20 total peaks -- but this is not what is happening, correct? And that is because of what I quoted in the first paragraph, particularly the word "unique". Am I understanding this correctly? Any further insights or explanations would be appreciated!
