MACS2 output (fold enrichment)

Question

[samantha_jeschonek]

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?

Answer 1

[BioinfGuru]

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 :)

[samantha_jeschonek]

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

[roma]

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

Answer 2

[roma]

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