Question: How run MACS2 with Pan Troglodytes (Chimp) genome?
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gravatar for LuisNagano
3.2 years ago by
LuisNagano20
University of Campinas
LuisNagano20 wrote:

I want to run the peak calling from MACS2 with the Pan Troglodytes (Chimpanzee) genome, but in the MACS2 manual, there are only 4 genomes to use (hs, mm, ce, dm) in -g, how must I run MACS2 for chimp genome?

ADD COMMENTlink written 3.2 years ago by LuisNagano20

It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromsomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size.

ADD REPLYlink written 3.2 years ago by Sinji2.9k

MACS2 should accept the -g parameter expressed as actual number rather than one of the 4 strings that denote the species for which the effective genome size was pre-calculated.

The chimp genome size is around 3.3e9 (a bit larger than human). Going with assumptions and estimates, if you assume the effective genome size to be 70% (as is for mouse) then you would specify -g 2.31e9; if the effective genome size was 90% (as is for human) then you would specify -g 2.97e9.

In all this, I wouldn't really know how to simply calculate the effective genome size (in fact, wouldn't it depend on read length?). I just saw this post which maybe talks about this: Effective genome size of UCSC hg38

ADD REPLYlink written 3.2 years ago by Marge280
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