Collapse all 7 taxonomic levels at once

[Gabriel_Pires]

Hi,
I’m a new QIIME2 user, I am trying to get the OTU table of relative abundances for all 7 levels at once but as I understood, the qiime taxa collapse script outputs a table for only one given level (passed into arguments), is there any other scripts that does the job for all taxonomic levels at once ?

Thanks for your reply.

[Nicholas_Bokulich]

Welcome @Gabriel_Pires!

There is no single command, but it would be relatively easy to use a loop, e.g., in bash to collapse at each level. Something like this:

for i in {1..7}
do
qiime taxa collapse \
    --i-table table.qza \
    --i-taxonomy taxonomy.qza \
    --p-level $i \
    --o-collapsed-table table-L$i.qza
done

If you really want all of them in one table, use “merge” to merge them.

Good luck!

[Gabriel_Pires]

Ok, thank you for your quick answer. Does this kind of analysis (per taxonomic level) is recommended ? Or should we just take into consideration the 7th level, i.e species level ?
If I recall well, QIIME1 did gave the OTU tables with all 7 taxonomic levels and their relative abundances at once !?

[Nicholas_Bokulich]

@Gabriel_Pires

Does this kind of analysis (per taxonomic level) is recommended ? Or should we just take into consideration the 7th level, i.e species level ?

In my opinion, no, looking at each taxonomic level is not necessarily valuable.

But it depends entirely on your question, of course! In my opinion it is most informative to look at ASV and species levels, perhaps also genus/family (again depending on your question).

I would let this be guided by a specific hypothesis, e.g., are you actually interested in genus/family level differences? Looking at higher levels, e.g., phylum, may not be suitable unless if you have a focused question, as discussed here:

ANCOM rejects null hypothesis at many W values that are 0

Hi @fgara, Glad it helped! Some of this is anecdotal. I suspect that if you go back to that earlier analysis and look, you’ll find a set of specific features that drive that phylum level difference. (It’s also worth keeping in mind that taxonomy is nested.). I dont think its a great example of a paper or how to do analysis, but if you look at Table 3 of this study, and you look up the taxonomy associated with each level, you’ll find that it’s nested and the difference in Fusobacteria is drive…

@Gabriel_Pires

If I recall well, QIIME1 did gave the OTU tables with all 7 taxonomic levels and their relative abundances at once !?

Times have changed I suppose — the analyses that developers deemed useful in the design of qiime 1 (a decade ago!) are not all state of the art in 2020. That is not to say that it is wrong per se, just that the field has evolved and it is recognized that, e.g., phylum-level information is often not revealing... and ASV-level analyses are now possible.