I read that control is important to get reliable peaks when using MACS2. However, I do not find any control for my treatment regarding the experiment that I am analyzing. I am using one dataset found in Chip Atlas and they get peak calling reports for the sample. But I do not know how do they define this control. The paper mentioned they used MACS2 but no explicit input controls were given. How is usually the best way to proceed when you lack this information without biasing the results or doing too much data manipulation? Thank you in advance for any helpful information.
GTN provides at least couple tutorials for MACS2
Hope it helps.
Thank you Igor. I will have a look at it.