Problems with q2-quality-control using Mockrobiota

[Nicholas_Bokulich]

Hi @xchromosome,
I think you took a wrong turn pretty early on. It sounds like you were taking the fastq sequence data from mockrobiota, processing it, and then attempting to use that as the "expected composition"? That's not correct — those data are essentially the equivalent of your own, being "observed" compositions of that mock community following some sequencing protocol.

Instead, you need to find the "expected taxonomy" file for that mock community and import that as a relative frequency table.

See this tutorial; it is using a fungal mock community but gives you a good idea of how the "expected taxonomy" from mockrobiota should be used:

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QI…

@xchromosome

All I wanted was a nice graph showing theoretical composition of my mock community vs Qiime 2 output, but I can probably do that myself in Excel and I won’t get that from q2-quality-control anyway, will I?!

yeah, q2-quality-control will show you actual accuracy scores (excel will not), but it will not make a bar chart of the compositions (excel will). You could do this with QIIME 2 taxa barplot, but it would take several steps to get your data in an appropriate format:

1. filter your feature table to only contain the mock community(s)
2. import the mockrobiota expected taxonomy as a feature table
3. merge the filtered and expected tables
4. make a modified taxonomy file for the expected taxonomy table. You would take the same expected taxonomy you used but copy the columns so you get something like this:

feature-id	Taxon
Bacteria;blah;blah;blah	Bacteria;blah;blah;blah
Bacteria;blah;blah;blah	Bacteria;blah;blah;blah
Bacteria;blah;blah;blah	Bacteria;blah;blah;blah

5. import that modified file as FeatureData[Taxonomy]
6. merge the taxonomy file for your observations with that modified taxonomy file
7. run qiime taxa barplot

Sorry! Not a direct route. mockrobiota was made in a pre-QIIME 2 era and has not been updated yet to conveniently mesh with QIIME 2; and QIIME 2 was certainly not built to cater to the needs of QIIME 2. One day this integration will occur...