Hello - complete newbie here. Trying to generate alpha and beta diversity core metrics from my data that I received today. I want to apply the command: qiime diversity core-metrics-phylogenetic
however I am not sure how to generate the requisite qza files needed as inputs
What I have is a OTU table (.txt) formatted as such:
OTU ID sample… sample… sample… … sample_
a metadata file formatted as a .tsv that looks like the one from the tutorial
and a fasta file (unaligned) (.fa)
Sequences were processes with dada2 v 1.8 and bacterial taxonomy was assigned from the Silva training set silva_nr_v132_train_set.fa.gz. Data is unfiltered.
I'd suggest converting your data to biom, using the command, biom convert. This is outside of QIIME, but will get the data properly formatted. So, for instance, if my table is otu_table.txt, then I would run the comamnd,