Chip-seq peak calling best way usage of parameters

Question

[luckysardar171]

Hello, currently working on chip-seq analysis calling peaks using MACS2, need suggestions how to set parameters according to my data i have H3K4me1 H3K4me3 and on MLL1 chip data for first two sample broad peak calling and MLL1 have to do narrow peak calling is it right way of doing and what parameter to set I am little confused because different parameter giving me different results peaks number how to choose best parameters value on my data. new to chip analysis(I have both single end paired end chip data) any suggestions

Thank you

[ATpoint]

Since these are both narrow histone marks the defaults should to fine. Maybe set the minimum peak length parameter to something like 200 to avoid very short peaks that are (probably) not really reliable.

[luckysardar171]

I did it like that, but peak numbers are differs to much, how to check how many common peaks between two parameter