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.
From my understanding, this dataset is ready to proceed with steps outlined in https://docs.qiime2.org/2018.11/tutorials/overview/#diversity-analysis. However, I am not able to generate the artifact files necessary to move forward (table.qza) as I do no have EMPSingleEndSequences sorted taxa.
Any idea how I would proceed? Or is it not possible with what I have been given?
Thanks for any help!