MACS usage for IgG and treatment
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6.9 years ago
TriS ★ 4.5k

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 :)

MACS ChIP-Seq normalization • 1.7k views
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6.9 years ago
Ryan Dale 4.9k

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.

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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!

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

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