macs2: how to retrieve normalized counts

Question

[olechnwin]

Anyone knows how to get the normalized counts for the ChIP-seq peaks using MACS2 ?

I would like to get the count of reads in the peak's region after normalization in both input and treatment (ChIP pull down).

MACS2 generates the treat_pileup.bdg and the control_lambda.bdg. What exactly is this? Can I use these files to extract the information to get the pileup (normalized read counts) in the entire peak region and not just at the summit which was outputted in the peak.xls file.

Thank you in advance for your help.

Answer 1

[ATpoint]

You could take the bed file (narrowPeak or broadPeak) that contains the peak regions and then use BEDtools intersect or BEDtools coverage together with your sam/bam/bed file that contains the sequencing data to get counts per peak. Then simply normalize these counts by, e.g. reads per million or any appropriate scaling factor.