Hi all,

I have a few bigwig ChIP-Seq files downloaded from ENCODE and visualized on IGV. These are histone H3K4me3 and H3K27Ac ChIP-Seq data. However, I loaded the respective narrow bed and bigBed files, and noticed that they did not call some of the smaller peaks observed in the bigwig file.

I am interested in the 'peak' boxed in red.

I have a few questions:

(1) Does that mean those small peaks that were not called are false positive? Or might they be present but at a smaller significance?

(2) Is there any software I can use to calculate the smaller peaks z-score? If so, how do I get those peaks to be called? Although the peak I am interested in only has a 100bp resolution...

Thank you and I greatly appreciate any inputs!