How to build an OTU table

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”

Hi @neocat,

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 :qiime2: 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.


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