Handoff to Qiime1 and phyloseq

[Gil_Sharon]

Hi All,

I’m trying to find the best way to combine analyses generated in Qiime2 with some functionalities from Qiime1 and Phyloseq. for than, I need the taxonomy table exported. Is there an easy way, like what’s present for the biom table and phylogenetic trees, to do so (in a way that conforms with the taxonomy table format in Qiime1) ?

Thanks!
Gil

[thermokarst]

Hi @Gil_Sharon! You can export your taxonomy (or any Artifact for that matter) by running qiime tools export:

# An example, using some test data I have hanging out on my laptop!
$ qiime tools export ~/moving-pictures/taxonomy.qza --output-dir ~/Desktop/taxa-data
$ cat ~/Desktop/taxa-data/taxonomy.tsv
Feature ID      Taxon   Confidence
d12759fe8dda1d65fe9077cc1ca9cf28        k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__[Weeksellaceae]; g__Chryseobacterium; s__     0.9986819789023034
5ada68b9a081358e1a7d5f1d351e656a        k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Leptotrichiaceae; g__Leptotrichia; s__   0.9999999985015222
d9095748835ade1b8914c5f57b6acbcf        k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Aeromonadales; f__Aeromonadaceae; g__Oceanisphaera; s__      0.9376999679084712
e83fa923d1e185d9c9de13ca3b37c8f2        k__Bacteria; p__Bacteroidetes; c__Cytophagia; o__Cytophagales; f__Cytophagaceae; g__Flectobacillus; s__ 0.999946340028078
bc15061b61cf6b5002c58284591f97d4        k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__; s__    0.9994429020230359
e063d1c3c9daf7390e5475e48d9b01c5        k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Lachnospira; s__    0.999998858876066
47fe572ed6a6b1d5f4a60a3884ec72e1        k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Paenibacillaceae; g__; s__    0.994845506178838
...

Depending on where you want to use this TSV table, you might need to remove the header row (e.g. QIIME 1, phyloseq)

Also, if you are interested in annotating a BIOM table with these data, you could export the FeatureTable, in addition to the data exported above, and use the biom add-metadata command to annotate the BIOM table.

Good luck, keep us posted!

[Gil_Sharon]

Thanks, @thermokarst!

I suppose the feature table also has the sequence for each of the amplicons?

[Gil_Sharon]

Never mind - got it (tutorials are a bit convoluted, but very very good, thanks! )

[thermokarst]

Alright @Gil_Sharon! If you have thoughts on how to structure the tutorials, feel free to open a new thread, we would love to get your input! If you haven’t seen this already, please check out the “Getting Started” guide - this is our suggested “flow” for getting to know QIIME 2! Thanks!