I have a fairly simple question regarding bedtools.
I've been asked to find the intersections between two types of sample peaks (ChIP-seq peaks). The goal is to see if they're similar or not (i.e. can we use our new method if it gives similar results/peaks to our old method).
I've used the following formula to find the reproducibility:
bedtools intersect -u -a sample1.bed -b sample2.bed -wa | wc -l
I then took the intersection value and divided it by the total of -a (sample1) to get the reproducibility rate. In other words, I'm showing the % of peaks in sample 1 that are reproduced in sample 2.
How would I interpret these results to a wet lab scientist if the reproducibility (overlap) is > 60%?
From my understanding, anything > than 60% (overlap) reproducibility is considered a good score because it's less likely to have occurred by chance?
Would I need to calculate a p value to show that there is a really good overlap?