Figure 3c). Indeed, 835 out of 1,684 ChIP-Seq specific peaks could also be detected in ChIP-chip, when the less stringent FDR cutoff of 5% is used. Another reason why peaks detected by ChIP-Seq may be undetected by ChIP-chip is that ChIP-Seq specific peaks are usually slightly shorter than similar fold-enrichment peaks found by both ChIP-Seq and ChIP-chip (Figure 3d) and may not be detectable on the array due to insufficient probe coverage. On the other hand, ChIP-chip specific peak regions also have significantly more sequencing tags than the genomic background (Wilcoxon p-value <10-320; Figure S2 in Additional data file 1), although with current sequencing depth, those regions cannot be called as peaks.
