I have three replicates for my ChIP-seq data, i did peak calling using MACS2, now i was thinking to get the common peaks from all the replicates which in my sense can be called as significance peaks. Now i have some questions 1. Which tool or algorithm should i use to do that and also i used "bedtools intersect" for getting overlapping peaks but the problem is after getting final bed file with common peaks i'm getting some redundancy in the file as intersection was done as per coordinates of the peaks and also for motif analysis which summit position should be used as after intersection it is very tough to understand. 2. As all the files has different summit position which summit positions should be used for motif analysis.