ChIP model peak and change mfold

[Nawal Chehab]

Hello,

How can i change MACS parameters in the ChIP pipeline?
I tried to make a configuration .ini file but not sure how to format it, both these did not work:

[macs2_callpeak]
nolambda = FALSE      
nomodel = FALSE      
mfold = 10 30

and 

[macs2_callpeak]
other_options = --nolambda FALSE --nomodel FALSE -m 10 30

As it is, visually, the highly significant peaks are due to the input being enriched within the area around it but looks very similar to the IP. The medium significant peaks are the real peaks where the surrounding input and IP are similar but the an extra skinny peaks stands out in the IP.
Therefore i would like to see the peak model and change some parameters.

Thank you!
Nawal 

[Alain Pacis]

Hi Nawal,

Thanks for your message.

Would it be possible to send me a UCSC track link (if available) or screenshot of your tracks.

For example: https://genome.ucsc.edu/s/apacis/Bahia_ChIP-seq

I need to see your peaks.

You can email at alain...@mcgill.ca

Best,

Alain