Good morning to everyone,
I’d like to obtain a FeatureTable[Frequency] object (like the one obtained from
dada2 denoise-paired) with actual taxonomy identification rather than a self-assigned name made up of a sequence of numbers and letters (like the one below).
Of course, at this step of the analysis, taxonomic identification hasn’t been performed yet, but it is done later, and I’m not sure how to obtain such table…
I’ve already checked out this previous thread and had already tried it as a part my pipeline, but I’d like to obtain a full file, without performing collapsing through
qiime taxa collapse at any taxonomic level.
This would make the results of any further analysis definitely more readable, without having to group my taxa at a specified level (but having a general overview of how my taxa behave instead).
I’ve noticed the plugin
qiime taxa barplot outputs a plot showing taxa rather than the previously mentioned codes, requiring a previously created taxonomy.qza file as input, but other plugins I used (like
qiime taxa filter-table to remove mitochondrial and chloroplastic contaminant reads from my features) will just use taxonomy to perform filtering, still outputting a FeatureTable[Frequency] containing the codes.
In particular, I’d be interested in obtaining such table, free from contaminants, showing taxonomies rather than codes.
Is there any easy way to perform this, starting from the filtered table obtained from
qiime taxa filter-table and the taxonomy.qza file resulting from
qiime feature-classifier classify-sklearn?
Thanks in advance!