Thank you very much for this tutorial.
I am having an issue when using qza_to_phyloseq. My ‘phy’ data is missing 1 sample; it contains 33 samples and there should be 34. This is the code I used:
phy<-qza_to_phyloseq(“table.qza”, “rooted-tree.qza”, “taxonomy.qza”,“sample-metadata.tsv”, tmp=“C:/tmp”)
I have no problem using the second option you provide with phyloseq though.
I am not sure what I am doing wrong with the qza_to_phyloseq command. Do you have any suggestions?