I am doing a metagenomic analysis on Galaxy with the pipeline FROGS. Everything works very well but I have a question for which I could'nt find the answer on the FAQs or anywhere... Briefly, I would like to compare my samples and, thereby, I would like to have the same number of sequences per sample. In the step "Affiliation stat", the software makes rarefaction curve. Does it calculates the minimum number of sequences for which the diversity is well represented for all the samples, and if so, where could I find this value? Does it use this number to subsampling the dataset for the abundance counts? Or do I have to subsample myself the dataset to have the same numbers of sequences per sample at the end of the analysis (and, if so, how could I subsample my sequences just before the affiliation step)?
Thank you in advance for your help, Maïlys.