Taxonomy analysis

[cesteban (Cristina)]

Hello,
I’m confused about taxonomy analysis in the new qiime.
I’m working with qiime only in the assign taxonomy analysis.
I have clustering results from another software (CROP), and in qiime1 I usually run :
1) assign_taxonomy.py with my crop.cluster.fasta
assign_taxonomy.py -m rdp -i allReads_crop.cluster.fasta -o tables_allReads -c 0.8
2) make_otu_table with cluster.list and the tax_assignmet which is resulted in the previous step,
make_otu_table.py -i allReads_crop.t.cluster.list -o tables/allReads.biom -t tables_allReads_crop.cluster_tax_assignments.txt -m metadata
3) convert in a biom file and sumarize taxa.
biom convert -i tables_allReads.biom -o tables_allReads_taxa.tsv --to-tsv --header-key taxonomy

In qiime2 I test the tuttorial https://docs.qiime2.org/2017.11/tutorials/moving-pictures/#taxonomic-analysis, I obtained taxonomy.qzv using my imported artifact (crop.cluster.fasta.qza imported with FeatureData[Sequence]), but I don’t know how to obtain the table.qza. In this tutorial steps I don’t see any step that it use my cluster.list
Could you help me please?

Thanks in advance,
Regards

[Nicholas_Bokulich]

Hi @cesteban,
Thanks for asking! If you are only performing taxonomy classification in QIIME2, then there is no need to import your cluster.list as a FeatureTable[Frequency] artifact.

Taxonomy information is not held within feature tables in QIIME2, and OTU cluster maps are not a data type that is currently handled in QIIME2 (though we have an open issue to add for support this in the future), so there is no equivalent command to make_otu_table.py. To use your pipeline outside of QIIME2, you must export your taxonomy information and then use that qiime1 command or another command to add taxonomy information to your biom table.

However, if you want to utilize the other cool analyses in QIIME2 , you could run make_otu_table.py without taxonomy information to generate a biom table, and import that biom table into QIIME2 as described here.

I hope that helps!

[cesteban (Cristina)]

Thank you very much for your quick response.
All right, I will use qiime1 to create my feature table and then import it into the new qiime to continue my analysis. I understand that when I import the biom table, it is my feature table (what you call in the tutorial-Moving-pictutable. qza), and from it I can do, for example, diversity analysis.

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny rooted-tree.qza \
  --i-table **table.qza** \
  --p-sampling-depth 1109 \
  --m-metadata-file sample-metadata.tsv \
  --output-dir core-metrics-results

Could you confirm that this is the right thing to do?

Regards

[Nicholas_Bokulich]

Hi @cesteban,

@cesteban

I will use qiime1 to create my feature table and then import it into the new qiime to continue my analysis

@cesteban

I understand that when I import the biom table, it is my feature table

Correct — a "feature table" is what one might call an OTU table in qiime1, but is a more general and inclusive term that we use instead for the reasons that I describe here.

@cesteban

and from it I can do, for example, diversity analysis.

Correct — once you have your feature table, you can use it for diversity analysis (e.g., with the command example that you posted), and many other analyses as described in the tutorials and the available plugin documentation. Any plugin that accepts a FeatureTable[Frequency] as input can be used with that feature table! (and other functions exist in the feature-table plugin to convert feature table data into other formats, e.g., for methods that take FeatureTable[RelativeFrequency] format artifacts).

Those tutorials are the best starting point for any new user of QIIME2, but since it sounds like you are transitioning from using QIIME1, various other guides in the documentation may be useful for you, e.g., getting started can help orient you with the new concepts and methods in QIIME2.

Happy QIIMEing!

[cesteban (Cristina)]

Thank you for everything. That’s been a great help