How to build an OTU table

[neocat]

Hi! I am very new to qiime2. What I want to achieve, starting from fastq I want to build an OTU table where each row corresponds to a position in a taxonomic tree (*), and each column to the raw count in a sample. Where each column corresponds to a sample. I worked through the “moving pictures” tutorial (the DADA2 branch). I looked at the resulting taxonomy.qzv / taxonomy.qza but it only seems to contain Feature ID, Taxon, Confidence. Shouldn’t there also be columns for the actual counts, and total counts for normalization? Is there a separate tutorial how to get to an OTU table? Or what is the most straightforward way to go from fastq to OTU table?

Motivation: I have several data sets from different studies that I want to compare. But my concern is, as these originally have been processed using different techniques, I cannot tell if differences between studies are caused by the processing or by the biological data. So I want to re-process each study using the same workflow.

(*) For example: “k__Archaea; p__Crenarchaeota; c__Thaumarchaeota; o__Nitrososphaerales; f__Nitrososphaeraceae; g__Candidatus Nitrososphaera; s__SCA1145”

[SoilRotifer (Mike Robeson)]

Hi @neocat,

@neocat

I looked at the resulting taxonomy.qzv / taxonomy.qza but it only seems to contain Feature ID, Taxon, Confidence. Shouldn’t there also be columns for the actual counts, and total counts for normalization?

This is intended. If you work through the tutorials again, you'll notice that the feature-table (i.e. the counts table) is kept as a separate file from the taxonomy. I suggest reading through the overview, for more details.

If you'd like to take a quick look at an old-style QIIME 1 like table, you can run the following commands:

qiime feature-table transpose \
    --i-table table.qza \
    --o-transposed-feature-table table-transposed.qza

qiime metadata tabulate \
    --m-input-file table-transposed.qza \
    --m-input-file taxonomy.qza \
    --o-visualization counts-and-taxonomy.qzv

Then view the counts-and-taxonomy.qzv on QIIME 2 View.

Protip: you can add multiple --m-imput-files as long as they share a common ID.

-Cheers!
-Mike