Hi! I am beginning to use Qiime2 and I analyzed a HiSeq dataset based on the tutorials. However, I still have some questions about the rarefaction of the data. Since I’d like to have the taxonomic analysis rarefied by the number of sequences, I applied the following command before the diversity analyzes:
qiime feature-table rarefy --i-table table.qza --p-sampling-depth x --o-rarefied-table rarefied-table.qza
However, I have to add the same value again when doing diversity analyzes, since the parameter --p-sampling-depth is required.
I have two doubts:
1 - Is this correct? Is this the best way to rarefied my data before the downstream analysis?
2 - Why does the taxonomic analysis of Qiime2 does not consider this value? Should data from Dada and Deblur be treated differently than 97% OTUs?
Thank you!