Hi there,
I am currently working on an ITS dataset that I would like to do alpha diversity on in R.
For my 16S diversity analysis, I usually go ahead and use the rarefied table produced as part of the core-metrics pipeline but I'm not sure how to get this for my final ITS OTU tables - I can't see how any of the filtering techniques described would work to rarefy, I even tried a few.
I haven't found anything so far in my searches here that allows me to properly rarefy the qiime2 output tables after taxa assignment. Does anyone have any suggestions/help please?
