Variability due to peak calling algorithms. We compared the average proportion of overlapping peaks identified by two ChIP-seq peak callers (red) and two ChIP-chip peak callers (blue) for the ChIP-seq and ChIP-chip profiles, respectively. Interestingly, the variation in peak identification concordance due to the use of different algorithms can be as large as technological differences, which is especially clear in the comparison of CBP and H3K27Me3 profiles.
Ho et al. BMC Genomics 2011 12:134 doi:10.1186/1471-2164-12-134