MACS usage for IgG and treatment

Question

[TriS]

hi all

this is probably a silly question but I prefer to ask...I'm using MACS for peak calling and differential enrichment between two conditions.

I have IgG and my antibody pulldowns in treated and untreated conditions...

intuitively, I should normalize the Ab signal to the IgG signal and then see the difference between treated and untreated conditions...but how can I do this in MACS?

I can get the enrichment of 1) my Ab vs IgG or 2) Ab-no-treatment vs Ab-treatment but in 1) I get the enrichment within the sample and in 2) i don't normalize for IgG

...what are your thoughts?

thanks :)

Answer 1

[Ryan Dale]

I'm not sure it's possible with MACS2, but you could also try alogrithms that are built from the ground up for this sort of thing, e.g.,

• PePr (paper, code)
• MultiGPS (paper, code)
• ODIN (paper, code)

(see ChIP-Seq: Calling peaks with replicates for more discussion)

By the way, be careful installing ODIN. It requires an older version of scikit-learn, so be sure to install it into an isolated environment if you use Python for other things.

[TriS]

Thanks Ryan

I contacted IT to install PePr and MultiGPS on our servers, those sounded like the most appropriate for what I need to do!

[ManuelAllh]

We have fixed the issue with scikit-learn. You can now install ODIN straight away, see http://www.regulatory-genomics.org/odin-2/basic-introduction/