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