Manage replicate samples and time point data

Hello, I am confused about replicated data. I have data which contain 100 individual, each individual contains 5 replicate samples with 2 time-points. The total number of samples is 500 samples. Now, I finished run the preprocessing step and cluster.split command. I am going on to analyze step of OTUs analysis.

My problem is I’m not sure that I should use command (with design file) to merge in each individual in first and run make.shared, classify.otu and so on follow in Miseq tutorial or not merging group in design file but use other statistic to evaluate samples in visualization step (such as taxonomy output, should I find average relative abundance in each individual?) Could you please any suggestion?

Thank you very much

I would not merge groups. keep those replicates separate for statistical analyses. You could average them if you are making a stacked barplot. If you are using R, feel free to use my generic data exploration script as a starting place

Thank you very much for your suggestion. Normally, I used R for visualization. I will try to use this. ^^

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