Diversity analysis with otu table and taxonomy data

[Nicholas_Bokulich]

Hi @pumpkin,
Thanks for posting!

@pumpkin

it seems that the biom file doesn’t contain the taxonomy

Feature tables in QIIME2 do not contain taxonomy, and will be discarded upon import. Taxonomy is contained in a separate FeatureData[Taxonomy] artifact. If you or your collaborators have a list of taxonomy assignments for each feature ID, you can import a file in the following format into qiime:

Feature ID	Taxon
229854	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Legionellales; f__Legionellaceae; g__Legionella; s__
367523	k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Flavobacteriaceae; g__Flavobacterium; s__
239330	k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfuromonadales; f__Geobacteraceae; g__Geobacter; s__

Import like this:

qiime tools import \
  --input-path taxonomy.tsv \
  --output-path taxonomy.qza \
  --type 'FeatureData[Taxonomy]'

Alternatively, if you only have the reference sequences associated with each feature ID, or want to classify using the taxonomy classifiers in QIIME2, import as described here.

@pumpkin

When I play the following code

biom validate-table -i feature-table-v210.biom

Unknown BIOM type: Table

The input file is not a valid BIOM-formatted file

This is an issue with BIOM formats and out of scope of the QIIME2 forum — you can get support with BIOM on the qiime 1 forum (the issue is probably that you have an old version of biom installed or need to specify the biom format (e.g., 2.1.0) that you are using).

@pumpkin

Error: Visualization viewing is currently not supported in headless environments.

It sounds like you may be trying to visualize on a remote computing cluster? E.g., see this post for more details.

@pumpkin

When I import it into qiime2, what I get is just the feature ID and taxon

Perfect — sounds like you already figured out how to import FeatureData[Taxonomy] as I described above (I've left that advice there in case I misunderstood your post). This is how taxonomy information is handled in QIIME 2. If you want to visualize taxonomic abundances in a barplot, use barplot. If you want to collapse your feature table to taxonomic groups and use those groups for downstream analyses, e.g., testing whether taxa are differentially abundant between groups, use collapse and proceed with other commands.

I hope that fixes all of your (non-BIOM-related) problems! Please let us know if these do not resolve the issues you are having.