I am trying to call RNA-Protein interation peaks by using Piranha software. I have multiple replicates for each experiment and the control data, and I can't seem to understand how to combine them into one Piranha query.

For example, if I was to call peaks using MACS2 software, I would probably type something like

macs2 callpeak -t exp_rep1.bed exp_rep2.bed exp_rep3.bed -c input_rep1.bed input_rep2.bed input_rep3.bed,

but after looking through the docs of Piranha GitHub repo I haven't found anyhing related to whether multiple replicates can be called at once or not.

I suppose if I know that the experimental replicates are somehow same between one another, I can just combine them into one file, but since I don't know for sure I don't want to spoil everything by doing this. Does anyone have an experience of calling RNA-Protein peaks having multiple replicas and if so, how do I solve this problem?