Thanks for the tutorial. I am mostly interested in the *.qza to phyloseq functionality. Having a bit of trouble with that. I get an error message using qza_to_phyloseq. Error in unzip(file, exdir = tmp, list = TRUE) : zip file 'DSEL16_whaleSIPABC_metadata.tsv' cannot be opened I am sure I don't j…

Hi Sebastian, The function only requires one file as a minimum. If you do not specify which files you are feeding qza_to_phyloseq it expects features, tree, taxonomy, then metadata (see ?qza_to_phyloseq). If I am correctly understanding, you do not have a taxonomy or tree file so you would need som…

Hi Jordan, that was very helpful, thanks a lot! I did have a taxonomy but was able to pull it into phyloseq using taxonomy="filename" along with feature and metadata as you described. cheers. Sebastian

If I may ask another amateur question.... My taxonomy is from Silva, so e.g. looks like this: OTU_4604 D_0__Bacteria;D_1__Spirochaetae;D_2__Spirochaetes;D_3__Spirochaetales;D_4__Spirochaetaceae;D_5__Spirochaeta 2;D_6__uncultured bacterium;D_7__;D_8__;D_9__;D_10__;D_11…

I would not recommend modifying the original qza file as this defeats some of the strengths of the format. Instead, I would manually import your taxonomy using read_qza() and work on the table itself, then manually build the phyloseq object from each individual qza as shown in the tutorial.

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