Visualizing/Classifying Reads After OTU Clustering

Hello,

I apologise if this question is quite basic, but I am very new to QIIME.

I am attempting to run the pipeline as described in the " Clustering sequences into OTUs using q2-vsearch" tutorial using trimmed fastq reads from the Human Microbiome Project T2D study (for one patient sample, ~30,000 reads). I followed the tutorial as described for closed-reference clustering, and obtained the output artifacts: table-cr-85.qza, unmatched-cr-85.qza, rep-seqs-cr-85.qza.

I was wondering how I can view/visualize/read these files in order to produce some sort of PCA graph that can be colored based on the determined OTU, or how to pass these files into alpha diversity calculations? I have tried opening the files using the QIIME 2 view, but I am not seeing anything particularly useful there.

Any help is greatly appreciated!

Thanks,
Camellia

Hi @camrae324,

Check out some of the other tutorials, e.g., the parkinson’s mouse tutorial, on the QIIME 2 tutorials website. This will show you how to run some different downstream analyses once you have a feature table… simply swap the feature table and rep-seqs in the tutorial (which are outputs of dada2 in that tutorial) with the table-cr-85.qza and rep-seqs-cr-85.qza that you have generated.

To run the diversity analyses you have in mind, qiime diversity core-metrics-phylogenetic is the command to look for in that tutorial

Note that since you used closed-reference OTU picking, you can use the reference taxonomy and reference tree instead of generating your own taxonomic classifications and phylogeny, if you so choose.

Yep, these are just artifacts (data files) so q2View will display basic info and provenance, but no visualizations.

I hope that helps!

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