I didn't make it, it appeared on Google while looking for examples of barplots including them...
For example, dada2 will remove reads that are errors or noise, but it will keep every read even if they cannot be assigned taxonomy.
I tried that strategy: I used dada2, followed by training classify-sklearn with 99% otus from GreenGenes, and then made the plot with the resulting taxonomy file. But as you can see there is no part of the plot referred to as 'Unassigned'. (Yes, those samples have a huge chloroplast DNA contamination and I'm just using them for training for now)
qiime dada2 denoise-pyro --i-demultiplexed-seqs sequenze/single_end2.qza --p-trunc-len 0 --output-dir denoise --verbose --o-denoising-stats denoise/denoising_stats.qza --o-representative-sequences denoise/representative_sequences.qza --o-table denoise/table.qza
qiime feature-classifier classify-sklearn --i-classifier gg_13_8/gg_13_8_otus/classifier.qza --i-reads denoise/representative_sequences.qza --o-classification taxonomy_dada.qza
qiime taxa barplot --i-table denoise/table.qza --i-taxonomy taxonomy_dada.qza --m-metadata-file metadata.tsv --o-visualization taxa-bar-plots_dn_99_dada2_OK.qzv
If you want to keep all your reads and still make OTUs, try
cluster-features-open-reference: Open-reference clustering of features. — QIIME 2 2019.7.0 documentation
or even better! Try this:
cluster-features-de-novo: De novo clustering of features. — QIIME 2 2019.7.0 documentation
I think I'm missing something, because I tried vsearch too, with all the three possible approaches, but no 'Unassigned' appears in the plots as well. Some may be VERY generic (Like 'Bacteria'), but no Unassigned ones.
It’s an interesting idea to show all your data (good data and errors, unpaired, and chimers) in a single graph.
Exactly, I'm particularly interested in this because I'd like to see (graphically) how many of my sequences remained unpaired though I could do that 'manually' by following these suggestions.