qiime taxa barplot without a table.qza but rather a rep-seqs.qza, is it possible?

[rosave (Rosa Vasquez Espinoza)]

Hi everyone,

I'm running metagenomics 16S experiments (V3/V4) on sediment samples. I'm doing a world comparison of similar ecosystems, and one of the locations of interest, did not have the fastqc files available, and rather only showed FASTA files fo the presentative sequences. I was able to import those into qiime to generate a sequence.qza file (without quality data) using the following command:

qiime tools import \
--input-path sequences.fna \
--output-path sequences.qza \
--type 'FeatureData[Sequence]'

I then took this sequence.qza file (no quality data) and MERGED it with a rep-seqs.qza file I obtained from fastqc samples from other parts of the world, using the following command:

 qiime feature-table merge-seqs \
    --i-data run1/rep-seqs.qza \
    --i-data run2/rep-seqs.qza \
    --i-data run3/rep-seqs.qza \
    --o-merged-data giant-merged-rep-seqs.qza

Now, I've performed taxonomy and want to visualize it in a bar plot.

However, to my understanding, this command below is the only one that works with bar plot in qiime (see below) which in my case it's not possible since I do not have a table.qza file for my FASTA original sequences as they were not denoised in this project. Any suggestions on how to create a visualization barplot from the tazonomy.qza file I currently have?

Thank you!

qiime taxa barplot \
--i-table table.qza \
--i-taxonomy test_taxonomy.qza  \
--m-metadata-file metadata.tsv \
--o-visualization test_taxa_barplot.qzv

[timanix (Timur Yergaliyev)]

Hello!
To create a taxonomy barplot in Qiime2, one need both taxonomy file and feature table. In feature table ASVs or OTUs counts are provided, which are essential for the barplot, meanwhile taxonomy information is taken from taxonomy file. Unfortunately, it is not possible to create taxabarplot without feature table.

[gregcaporaso]

@rosave, note that while you can't create the barplot without the table (because the abundance information is not included in the taxonomy file, as pointed out by @timanix), you can get a table of all ASV ids and the assigned taxonomic labels using qiime feature-table tabulate-seqs. That may or may not be useful, depending on your goals for this analysis.

Alternatively, if you have feature tables associated with each of your original rep-seqs.qza files, you could merge those with qiime feature-table merge, to get the feature table that you need for generated the taxonomy barplot.