I ran MACS2 for paired-end data using the following command: macs2 callpeak -t "$SAMPLE_FILE" -f BAMPE -g hs --keep-dup all -B --call-summits. One challenge I am facing is the large size of the m6A peaks. Typically, with paired-end data, MACS2 infers the peak size from the BAM file. How can I reduce the peak size to make the methylation comparison more precise ?
thanks
below attached the peak size distribution
thanks
below attached the peak size distribution