Normalisation using Input DNA & calling peaks [Chip-seq]
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3.6 years ago
anu014 ▴ 180

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!

ChIP-Seq next-gen normalization macs2 • 1.4k views
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Entering edit mode
3.6 years ago
Satyajeet Khare ★ 1.6k

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.

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