How can I increase the number of peaks using macs2 peak caller?

Question

[GK1610]

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?

[Devon Ryan]

What the others said, but why do you expect 150-200k peaks?

[Chirag Nepal]

In general it is not a good idea to call 150-200K peaks, as it will contain many false positive peaks. 35K peaks looks reasonable.

[Mike]

Agree with @Chirag Nepal, but you can change your criteria -p/q value for that.