Normalisation using Input DNA & calling peaks [Chip-seq]

Question

[anu014]

Hello Biostars,

We all know that macs2 uses 'global background' for normalisation in 'mascs2 callpeaks' command. But is it possible that we can use our own BAM file (Input DNA) for normalisation ? I have Treatment, Wildtype & Input DNA BAMs. And how to call peaks if normalisation is done?

Please help. Thanks in advance!

Answer 1

[Satyajeet Khare]

It is better that you have your own input sample. It is used as follows.

macs2 -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01

where -t is Treatment or Wildtype and -c is input.