I ran macs on my files and took out the peak summits for further analysis. But then I opened my files in IGV, and the position of the summit does not look like the highest point in the peak.
I ran the analysis again to make sure it was not some error I did, but got the same summits. Anyone have any idea what I did wrong?
macs2 callpeak -t IP.bam -c input.bam -f BAM -g 200000000 --bw 100 --keep-dup all --nomodel -n results -B -q 0.01