Taxon names missing in ANCOM results

[skimble]

Dear Forum:

I am in search of help with the ANCOM output. I have searched the forum but haven't found this problem. I've checked the glossary. I am running qiime version 2019.10.0 installed via conda.

When I run:

qiime composition ancom
--i-table ./taxonomic_analyses/table-dada2-wo_recaps_ITS_filtered_abund_comp.qza
--m-metadata-file ./denoised_without_recaps/TurtleMapITS_without_recaps_Adamovicz_metadata.tsv
--m-metadata-column Year
--o-visualization ./taxonomic_analyses/ancom_year.qzv

I get the expected .qzv file but I get feature IDs:

where I expected taxonomic names. Suggestions?

Thanks,
Steve

[sbslee (Seung-been Steven Lee)]

Hello @skimble,

In order to get taxon names from ANCOM, you have to first collapse your features to a specific taxonomic rank. This is well explained in the famous “Moving Pictures” tutorial (click here to see the relevant section).

For instance, if you want to perform ANCOM at the genus level (I’m just copying and pasting from the tutorial):

qiime taxa collapse \
  --i-table gut-table.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 6 \
  --o-collapsed-table gut-table-l6.qza

qiime composition add-pseudocount \
  --i-table gut-table-l6.qza \
  --o-composition-table comp-gut-table-l6.qza

qiime composition ancom \
  --i-table comp-gut-table-l6.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-column subject \
  --o-visualization l6-ancom-subject.qzv

Hope this helps!

[Mehrbod_Estaki]

Hi @skimble,
While @sbslee’s excellent suggestion will allow you to view taxonomic names instead of the hashed featureIDs in the ANCOM output, I’d just like to point out that this approach is qualitatively different than using the ASVs and will likely yield different results. This is because the collapse function groups all of your features to a specific taxonomic tank, so even if species level is chosen, consider that many different ASVs can be collapsed into a single species. This will of course change ANCOM results.
To identify the taxonomy of those specific hashed IDs in your current results, you can copy their code and search for them in your ‘taxonomy.qzv’ artifact which you should have already made if you were following the Moving Pictures tutorial.
Good luck!