Cleaning phantom peaks
From the ENCODE3 QC suggestions, phantom peaks give cross-correlation values that may help identify if your chip-seq worked or not, and also gives numbers based on phantom peaks. However, is there any way to further remove these phantom peaks from the analysis (either before or after peak calling using macs2)?
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Try blacklisting them, or expunging / removing them from your input data? I have not used macs2 that much.