I’m working with Qiime2 since last month and I’m trying to understand the concept of rarefying and how this can affect my downstream analysis. A quick background: I have sequences generated from fungi that were colonizing plant roots. These plant species are known to be poorly colonized by fungi (low fungi biomass in my samples) therefore I did not expect much diversity.
I realized that for one plant species (samples Sa3 and Sa30) the maximum sampling depth was only 4000 whereas for the other species it was 7000 (Sa27) and 11000 (Sa1). When I first seen it, the first thought I had was that I cannot use this dataset like this in the downstream diversity analyses to compare both species (because of the differences in sampling depth). Am I thinking on the right way?
After that, I rarefied to 6000 and I still have enough replicates of each species for comparison reasons.
So, would be this the correct dataset to proceed with the downstream analysis?
Thank you so much for your attention!