I’m kinda new to QIIME2 and its pipelines, really enjoying the tutorials and the community though.
In my case I have a 16S dataset from an Ion Torrent. I’ve already accomplished to do the denoising of sequences and did two types of clustering: de novo and closed reference (using the Genome Taxonomy Data Base).
Now that I have my feature-tables, I would like to attribute taxonomic names to my OTUs in order to make that classic OTU-table. I’m kind struggling on that though. Should I use feature-classifier or taxa collapse? Does anyone have any tips?
The feature-classifier plugin will label / classify your reads with taxonomy. The taxa collapse is helpful for merging / collapsing your features after you have assigned them taxonomy.
We cluster sequences to collapse similar sequences (e.g., those that are ≥ 97% similar to each other) into single replicate sequences. This process, also known as OTU picking , was once a common procedure, used to simultaneously dereplicate but also perform a sort of quick-and-dirty denoising procedure (to capture stochastic sequencing and PCR errors, which should be rare and similar to more abundant centroid sequences). Use denoising methods instead if you can. Times have changed. Welcome to the future.
Now that you have upgraded your Qiime, you can upgrade your analysis at no additional cost! Check out qiime dada2 denoise-pyro and welcome to the future!
