Question about permutation_callpeak

[MarLee39]

Hi,

Thank you for developing such a nice tool. I would really like to use CLAM in my project!
I am a newbie in this field, and currently trying to analyze RIP-seq data.

I have a question about peak calling. I processed my data using multi-replicate mode though, I am not clear whether I should also try permutation_callpeak command.
This command seems to process only one sample at a time according to your example, which means that I use this command when no multiple RIP-seq data is available? I have read your NAR paper, and struggled to understand the procedure, but it was a little bit difficult for me.

Hope you could help me for better understanding about the peak calling with CLAM.

Best,