How to compare the peaks called by MACS2 with the peaks called by ChIPOTLe?

Question

[s.singh]

Hi,

I have ChIP data of a histone variant from the male germline. I used MACS2 to call the peaks. I want to compare my MACS2 generated peaks with an already published embryo histone variant data but they have used ChIPOTLe to call the peaks in their analysis. Is it ok to compare those peaks? I am not sure because both peaks are generated via different platforms. Any idea about how to compare the two peaks?

I am annotating the called peaks using ChIPseeker.

Any help will be highly appreciated. Thank you! :)