Dear Natsuhiko,

Thanks a lot for the work on Rasqual, it is a great tool. I am working with ChIP-seq data, and would like to compute FDR.

I saw in a recent paper ( Schwartzentruber 2017) that authors performed one permutation and then estimated FDR. Do you have a recommendation on how many permutations to run? Also, if I understand correctly, this FDR will be for each peak. So, for reporting the significance of a given variant the reported BH q-value from Rasqual is sufficient, and FDR is calculated only to get significant peaks, right?

I know that this is more a conceptual question so I appreciate a lot your help and time.

Best,
Ariel