I found the result of macs2 is not perfect and I want to know why. Firstly, I briefly describe the ChIP I made: The sequencing files are paired-end. Because of poor sequencing depth, I merge two input and two IP sample into one input and one sample. After processing the raw fastq files, I used bowtie2 to map these reads. Then I used macs2 to call peak.
macs2 callpeak -t IP_mm10.bam -c Input.bam --outdir . -n IP -g 2652783500 -q 0.1 -f BAMPE --keep-dup all -B
Because I am interested repeat region, I retaind all duplicated. I found the effective genome size from deeptools for mm10. I think the process is OK, but the result is weird. The input file also has peaks, And the score is high.
The two files are bigwig files converted by bamcoverage. Is my code wrong?