Question

MACS2 output (fold enrichment)

0

Entering edit mode

6.5 years ago

samantha_jeschonek ▴ 50

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 • 6.7k views

ADD COMMENT • link updated 6.5 years ago by roma ▴ 120 • written 6.5 years ago by samantha_jeschonek ▴ 50

score 0 · Answer 1 · 2018-06-01

0

Entering edit mode

6.5 years ago

BioinfGuru ★ 2.1k

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 :)

ADD COMMENT • link 6.5 years ago by BioinfGuru ★ 2.1k

0

Entering edit mode

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

ADD REPLY • link 6.5 years ago by samantha_jeschonek ▴ 50

0

Entering edit mode

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

ADD REPLY • link 6.5 years ago by roma ▴ 120

score 0 · Answer 2 · 2018-06-01

0

Entering edit mode

6.5 years ago

roma ▴ 120

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

ADD COMMENT • link 6.5 years ago by roma ▴ 120