How are the taxonomic levels (at level 7) that are outputted in the taxa-bar-plots.qzv connected to the taxonomy.qzv? The taxa-bar-plots.qzv does not provide FeatureIDs only taxonomic levels. In my dataset, the same taxon levels (at level 7) correspond to multiple different FeatureIDs (at different confidence levels). How do I know which specific FeatureID corresponds to the taxonomic level displayed in the taxa-bar-plots.qzv?
I could not a find a Qiime2 artifact that links the specific FeatureID to the specific taxonomic level in the bar plot. It’s a bit confusing to explain but hope that was clear.
The taxonomy.qza file is the missing link. The barplots are intended to show taxonomic abundance (i.e., features sharing the same taxonomy are collapsed into one). These barplots are not intended to show the abundance of individual features (sequence variants) — there are bound to be too many features to meaningfully represent in a barplot. If you want to see the abundance of individual features, I recommend that you use
qiime feature-table heatmap instead.
Thank you for the quick reply. By collapsing features that share the same taxonomy, what does this mean exactly? Is it clustering at a certain percentage threshold? >97%? My goal is get the representative 16S rRNA gene sequence of the collapsed sequence variants shown on the barplots.
their relative abundances are summed to the relative abundance of that taxon that is represented in the barplot.
No — if two sequences share the same taxonomic classification, they are grouped.
There will not be one representative sequence. Multiple unique sequences may be classified as the same taxon, as you have observed. You can search for a taxon of interest in the taxonomy.qzv visualization that you have to find the sequences assigned to that taxon, but there is no way to group the sequences.
I hope that clarifies!
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