I recently made the switch from Qiime 1 to Qiime 2 and am enjoying the format and new ways of analyzing data. In one of my datasets I have taxa identified as "k__Fungi;;;;;;" and "k__Fungi;p__Ascomycota;;;;;__" that I would like to remove from the feature table. I tried the following with no luck: q…

Hi @wlandesman , Drop the empty semicolons — these appear when you view a barplot at a specific taxonomic rank (e.g., level 7) but those are not in the underlying taxonomy file (export the data if you want to see for yourself). You probably want to do something like this instead: qiime taxa filter-…

That did the trick - thanks! As a follow up, is there a way to get a list of the rep seq IDs for the sequence(s) placed in one of the unassigned taxa (i.e. the fungi;;;;;;)? I am curious to see if this unassigned taxa is a single or many different "OTUs". I suspect the latter but would like to confi…

See this tutorial . That will merge your sequences and their taxonomy classifications in a searchable visualization. Good luck!

Thanks for the suggestion. This leads to more questions, which I think are still relevant to this topic. Within the rep-seqs that are classified to "k__Fungi;p__Ascomycota__", but with no further taxonomic resolution, there are 185 rep seqs. Visually inspecting the entire phylogenetic tree of all da…

[image] wlandesman: Visually inspecting the entire phylogenetic tree of all data, I see that these taxa are found in different parts of the tree. Are these ITS sequences? Just want to make sure because ITS is a non-coding, non-phylogenetically-informative domain, and hence the tree will not r…

Thanks for your response and sorry for the long delay in getting back to you. This is ITS data and so I probably should not be looking at the tree, as you mentioned. However, since the "p__ascomycota" are spread throughout the tree, I think this is a clue that they are different genera/species. Ther…

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Filtering unidentified taxa from feature table

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