MACS2 output (fold enrichment)
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3.4 years ago

Hopefully a simple question --

Is the "fold enrichment" output from MACS2 callpeaks a straight fold enrichment or is is a log10/log2/ln fold enrichment?

macs2 macs chipseq • 3.6k views
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3.4 years ago
YaGalbi ★ 1.5k

From Github MACS2 README section "Output files":

NAME_peaks.xls: "fold enrichment for this peak summit against random Poisson distribution with local lambda, -log10(qvalue) at peak summit"

Good luck deciphering what that means :)

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Those are two different columns: 1) fold enrichment and 2) -log10(qvalue).

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3.4 years ago

Hahah, I did see that in the README, but it left me equally confused!

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3.4 years ago
roma ▴ 120

It is just a fold enrichment, yes. Otherwise it would be called log fold enrichment! ;)

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