I have a set of chip seq bam files.
I have ~ 24 million paired-end reads in these bam files
I used macs2 for narrow peak calling
macs2 callpeak -t $SAMPLE_1 -c $CONTROL --keep-dup all -f BAMPE -g hs -n $OUTPUT -B -p 1e-3
I am getting only 35K peaks. I expect to see 150-200k peaks. do you have any suggestions?