How to deal with replicates

Hello, I have three replicates ( rep1, rep2, rep3 ) and one (INPUT) control file of H3K27ac. I identified peaks with IDR tools.

I used the follow command to identify SEs

python ROSE_main.py -g MM9 -i peaks.gff -r H3K27ac.1.bam -b H3K27ac.2.bam,H3K27ac.3.bam -c INPUT.bam -o outdir -s 12500 -t 2000

Is this right? Merge those replicates? I am not sure which solution is suitable for SEs identification. So, how to identify super-enhancers from these replicates?

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