Macs Chip-Seq Contorl

Question

[Ming Tommy Tang]

Hi all,

for peaking calling with MACS I use

macs -t IP.bam -c Input.bam -n ChIP -g mm -B

I understand the control is the input control ( unchipped, but sequenced) how about the IgG control? can I use it in the command?

Thanks!

Answer 1

[Mikael Huss]

Sure. Just use it with -c instead of Input.bam. If you are asking about using both the input and IgG controls in the same MACS run, that is not possible as far as I am aware. It is in fact an interesting question to consider how to call peaks against both types of control. The rationale of using an input library is to correct for chromatin accessibility, and with the IgG library the goal is to correct for unspecific binding. As a simplistic strategy one could do two rounds of peak calling: IP vs. input and IP vs IgG, and select only the peaks that are found in both.

[Ming Tommy Tang]

Thank you so much! Then Is it possible to generate a bedgraph file with IP minus the IgG background?