I am analysing ChIP-seq data for histone protein.
The study is timeline study. It aims to study the binding pattern of histone at different time points(0hr, 2hr, 4hr, 5hr, 6hr). We have two strains namely virulent and avirulent for the time points (2hr, 4hr, 5hr, 6hr) and 0hr sample is common.
I hava few questions about analysis listed below:
1) I am doing peak calling with help of MACS2, What are the parameters to be consider for peak calling ?
2) I dont have Input and mock, should I use one of my sample as control during macs2 peak calling or I do peak calling step without control
3) what should be the minimum number of peaks discover in histone study