fseq2 callpeak_idr input

[mcsimenc]

Hi, this is not a bug report but a question about usage. The inputs for callpeak_idr are a treatment + control for each replicate. I have two control replicates and two treatment replicates but my controls aren't specifically paired with a given replicate, so can I provide both controls as input for callpeak_idr using each of -control_file_1 and control_file_2? If not, can you recommend how I proceed? P.S. I ran callpeak once for each replicate inputting both controls under -control_file. Thanks!