I have a ChIPseq of a TF (narrow peaks), without replicates, which peaks were found with a good quality using an INPUT dna as control. QUESTION: Is there any statistical way to validate the final list of peaks in the downstream analysis, in order to filter those peaks which are called as statistically significant, but when looked by eye in a browser the enrichment they present seems to be like background?
Below I put an example of what I'm describing in a region of 76 Kb region:
In the first pair of tracks, one could appreciate the enrichment of the TF (red) versus the input (black) highlighted as blue boxes. But in the second pair of tracks, the peak caller mark just the small peak in the center of the blue box (marked also with another track in black as a little profile, just above the peak). The statistical parameters used to get the peaks are pvalue < 10e-5 and FDR < 1%.