I would like to study H3K27ac modification in some stages. I have the below bam files and the number is read counts.
113,664,782 A.bam 87,305,342 B.bam 83,029,416 C.bam 49,539,212 D.bam
I used MACS2 to call peak:
macs2 callpeak -t $input -q 0.05 -f BAM -g hs -B --outdir $output -n $sample
and I get the peaks:
9065 A_peaks.narrowPeak 4873 B_peaks.narrowPeak 11080 C_peaks.narrowPeak 3521 D_peaks.narrowPeak
So the question is : why are the peak numbers so few? Is the sequencing depth enough or other reasons?