Generating an OTU table

Technical Support
1

Hello,

I have been using qiime 2-2022.2 to carry out my analysis. I want to know whether it is possible to generate an OTU table containing the OTU number and its abundance but without the taxonomy units assigned using qiime 2.

Moreover, I want to know how I can generate a table_abundance.tsv.

Also, I have used the denoised output file directly to construct the feature table and assign taxonomy. I want to know whether the procedure that I have followed is correct. The commands that I used are as follows.

qiime dada2 denoise-pyro **
--i-demultiplexed-seqs trimmed-seqs.qza **
--p-trim-left 15 **
--p-trunc-len 240 **
--o-representative-sequences rep-seqs-dada2.qza **
--o-table table-dada2.qza **
--o-denoising-stats stats-dada2.qza
qiime metadata tabulate **
--m-input-file stats-dada2.qza **
--o-visualization stats-dada2.qzv
mv rep-seqs-dada2.qza rep-seqs.qza
mv table-dada2.qza table.qza
qiime feature-table summarize **
--i-table table.qza **
--o-visualization table.qzv
qiime feature-table tabulate-seqs **
--i-data rep-seqs.qza **
--o-visualization rep-seqs.qzv
qiime feature-classifier classify-sklearn **
--i-classifier gg-13-8-99-515-806-nb-classifier.qza **
--i-reads rep-seqs.qza **
--o-classification taxonomy.qza
qiime metadata tabulate **
--m-input-file taxonomy.qza **
--o-visualization taxonomy.qzv

Thank you in advance,
Brigitta

2

Hi @Brigitta1,

(I am assume all the questions are related to the commands you show, please let me know if it is correct! )

On generating a feature table without the taxonomy units, the 'table-dada2.qza' artefact should have the info you are looking for and should not have any taxonomys assignemt in it. So, if I undersatand what you mean, if you export fom it using 'qiime export' command you should get a biom file, which in turn you can convert to feature.tsv by using the biom conversion utility (let us know if you need help for this.)

On your commands, they sound overall reasonable. For what I can note, few potential issues could be the following: in th edenoysing poyro step, you use 240 as trun-len parameter, did you check your quality profile to confirm if this lenght suites your sequences? I would expect a bit longer number for 454 data. For the taxonomic classification step, gg is not updated since long time, so it could be a good thing for you to use Silva too to compare the results. You probably want to use also the 'qiime taxa barplot' command to produce the barchart visualiser with th eobtained taxonomic information.

Hope it makes sense.
Luca

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