What parameter values to change in peak calling with MACS2 when calculating IDR afterwards?

Question

[salamandra]

To use IDR we need to relax peak calling settings when running MACS2. How do we do that? Is it enough to increase the qvalue threshold? Are there any specific parameter values we need to use?

[Kevin Blighe]

For MACS-related questions, you will likely get a response on the group's GitHub page, where the program athour is active: https://github.com/taoliu/MACS