search

macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
702 stars 268 forks source link

Q: Same parameters,but different peaks number #509

Open zhangpicb opened 2 years ago

zhangpicb commented 2 years ago

Hi @taoliu ,

Describe the problem callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B --SPMR -t TF.bam -c IgG.bam -n TF generate TF.narrowPeak files contain 6 rows. callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B --SPMR -t TF.bam -n TFwithoutIgG generate TFwithoutIgG.narrowPeak files contain 6067 rows.

It's a strange things that two narrowPeak files have a such big difference.

Describe the solution you tried

Using IGV to find why,but still confusing! The narrowPeak without IgG.bam Input have a peak,but the narrowPeak with IgG.bam Input doesn't have this peak.

igv png

Thanks in advanced!

taoliu commented 2 years ago

Hi @zhangpicb really strange, since I normally assume the opposite. Could you also load the 'bedGraph' files from MACS in IGV as well?

zhangpicb commented 2 years ago

Hi @zhangpicb really strange, since I normally assume the opposite. Could you also load the 'bedGraph' files from MACS in IGV as well?

Hi @taoliu

JPG