Is read coverage normalised to RPM or RPGC?

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MACS -- Model-based Analysis of ChIP-Seq

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Is read coverage normalised to RPM or RPGC? #193

Open jma1991 opened 7 years ago

jma1991 commented 7 years ago

When running macs2 callpeak with the flags -g GSIZE -B --SPMR are the bedGraphs files produced normalised to reads per million (RPM), or is the effective genome size included in the calculation (RPGC), similar to the normalisation used in the deepTools command bamCoverage?

chiefcat commented 6 years ago

@jma1991 Hi Jma, I want to ask this question too. Have you gotten any idea so far? Is there anyway to produce RPGC normalized bedGraphs by MACS2? Thanks!