Question: How can I increase the number of peaks using macs2 peak caller?
0
gravatar for GK1610
3.0 years ago by
GK161060
United States
GK161060 wrote:

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?

chip-seq • 1.8k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by GK161060
1

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

ADD REPLYlink written 3.0 years ago by Devon Ryan91k

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.

ADD REPLYlink written 3.0 years ago by Chirag Nepal2.2k

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

ADD REPLYlink written 3.0 years ago by Mike1.3k
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