I am relatively new to Chip-seq analysis and have a question regarding macs2callpeaks. Overall I managed to get peaks from my Chip-Seq data however I am a bit puzzled by the "normalization" of the peaks using a control file. We have a seq on H3K27ac with different conditions and each condition has a separate "Total". The question is; when I used a different total to normalize one of my conditions with a different "total", the bedgraph on ucsd genome browser looked exactly the same as it were if I normalized it with its correct respective "total". I did not expect much variability using the different totals but I did think there would be at least a small difference. I also tried to normalize one of my conditions(treatment) with another condition(as a control) to view it on the genome browser to see if maybe I did something wrong. However when i viewed it on the genome browser there was only a slight change in its peaks compared to the correctly normalized treatment/control. I would have thought that using another condition would brought down the peaks by a significant amount? I am just having trouble understanding how the treatment/control works in MACS2Callpeaks. Do I have to change the parameters? I apologize for the novice question.