I am comparing the output of two chromatin profiling methods.
So far I mapped my reads to the genome and compared the resulting bed files by using bedtools jaccard.
However, as the data in one track is rather noisy I fear that the bedtools jaccard score (calculated via overlapp) does not necessary represent the real, significant sample similarity. So is it advisable to perform peak calling before comparing?
I was also wondering if there is a "gold standard" for comparing two different ngs tracks?