Re: [macs-announscement] MACS2 for broad peaks

[Tao Liu]

K27me3 as a repressive mark is very weak comparing to other factors. So default MACS pvalue or qvalue is too stringent. You can try fold-change cutoff -- try to build signal track of fold change (https://github.com/taoliu/MACS/wiki/Build-Signal-Track) , then call peak from it (macs2 bdgbroadcall). Pol2 can be handled just like other active broad mark. -- try default

Best,

Tao

On Feb 21, 2013, at 1:34 PM, Alexander Predeus <pre...@gmail.com> wrote:

Hello all, 

I was going to try MACS2 for a series of Chip-Seq experiments that are known to have broad "signatures" (e.g. K27me3, Pol2, etc). 

Is there a suggested command that should be used with MACS2 for broad peak calling? What options (besides --broad) are a must-have or highly recommended? 

Thank you in advance. 

 -- Alex 

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Tao Liu

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