Start analyzing demultiplex fastq files.

I have a set of fastq files that are already demultiplexed.
I would like to run Qiime2 and create OTU tables showing the abundance of different species. I am struggeling to understand were I should start and which tutotial to use. I am also confused about the qza format.

Hi @Robin_Mjelle,

Welcome to the :qiime2: forum.

I'd recommend the Parkinson's Mouse tutorial as a starting place for you. This works from already demultiplexed sequences and goes through a variety fo analyses. (The moving pictures tutorial goes through a similar trajectory, but it starts from undemultiplexed sequences).

My recomendatation is to use amplicon sequence variants (ASVs) instead of OTUs. They're higher resolution, possibly even going to the strain level (at least in a recent study of mine). These are described in the tutorial linked above. If you decide for some reason that you want OTUs, I would recommend the OTU clustering tutorial.

Finally, I want to discourage you now from looking for species level abundance. Morphology-based names often don't have much to do with the evolutionary history of organisms, even in macroscopic organisms (look at :chicken: and :t_rex: if you don't believe me), let alone for things we can't culture or define as species. Get comfortable with OTUs/ASVs as molecular barcodes and have fun there.

Please let us know if you have issues as you work through the tutorials or with your data.


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