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”