DADA2--ASV number and taxonomic assignment

[amcrowell (Anna Crowell)]

I am coming in on the back end of a project involving Qiime. Some sequences that should have been removed made it through filters, but I didn’t notice them until I pulled the data into Excel.
I need a file that would contain ASV numbers and the taxonomic assignment in order to also delete these ASVs in the DADA2 table. When viewing the dada2.qzv, I do not see any ASV numbers or taxonomic assignments. Is there another step I need in order to create this file? Thanks!

[sbslee (Seung-been Steven Lee)]

Hi @amcrowell,

Wellcome to QIIME. If I understood your question correctly, you are looking for a way to visualize/tabulate the mapping between ASV IDs (feature IDs) and their taxonomic classifications. In order to to this, you need to create a visualization file. Click here to see an example file and see if this is what you want.

If above is what you want, I highly recommend that you go to the famous “Moving Pictures” tutorial from the QIIME team, and learn how to create such visualization files. The above example file is called taxonomy.qzv in the tutorial. Search for the file name (“taxonomy.qzv”) within the tutorial page.

You can go one step further by mapping ASV sequences, instead of ASV IDs, to their taxonomic classifications. As far as I know, there is no QIIME command to do this. When I had to this, I could not find any solutions, so I wrote myself a lightweight Python package called ‘Dokdo’ (GitHub - sbslee/dokdo: A Python package for microbiome sequencing analysis with QIIME 2) to do it.

You can simply clone the repository and then run the following command:

$ python3 path/to/dokdo/cli.py tax2seq taxonomy.qza rep-seqs-dada2.qza output.csv

You have already seen the taxonomy.qza file. The rep-seqs-dada2.qza file should have been created by DADA 2. Search for the file name (“rep-seqs-dada2.qza”) within the tutorial page for more details. The output file (“output.csv”) will contain the mapping between ASV sequences and their taxonomic classifications. For more information about the tax2seq command, click here for the docs.

The Dokdo package has some other useful functionalities, so take a look if you are interested. It is designed for QIIME 2 users. Let me know if you have any questions.

output.csv (205.3 KB)

[Nicholas_Bokulich]

Hi @amcrowell and @sbslee ,

@amcrowell

I need a file that would contain ASV numbers and the taxonomic assignment in order to also delete these ASVs in the DADA2 table.

Any "FeatureData[Taxonomy]" artifact (e.g., the output of a taxonomy classifier) would contain this information, mapping ASV IDs to taxonomic assignments. You can either export the data to use it outside of QIIME 2, or use "qiime metadata tabulate" to create a searchable QZV file to allow you to search for specific ASVs.

By dada2 table I assume you mean a feature table. You can use "qiime feature-table filter-features" or "qiime taxa filter-table" to filter ASVs from your table... e.g., specific IDs, taxa, or based on some other criteria. See the tutorials and help documentation for more details.

@sbslee

You can go one step further by mapping ASV sequences, instead of ASV IDs, to their taxonomic classifications. As far as I know, there is no QIIME command to do this

This is actually quite straightforward in QIIME 2 and is documented here:
https://docs.qiime2.org/2020.8/tutorials/metadata/#exploring-feature-metadata

That creates a searchable visualization and preserves the data provenance.

Good luck!