How to normalize the output.bdg

macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq

https://macs3-project.github.io/MACS/

BSD 3-Clause "New" or "Revised" License

698 stars 268 forks source link

Open JingxinGuo opened 7 years ago

JingxinGuo commented 7 years ago

Hi taoliu, Dose the macs2 normalize the values in pileup.bdg ? Thanks you very much.

dbrg77 commented 7 years ago

If it is from the "pileup" command, then it is not.

If it is from the "callpeak" command:

If you set "--SPMR" flag during the peakcalling, then it is normalised to 1 million reads. Otherwise, it is not.