Hei, I am trying to remove unwanted features from my feature table based on taxonomy. I have classified my features with the greengenes classifier and wanted to remove features with no assigned taxonomy or only assigned at the domain-level. I managed to remove most of them using qiime taxa filte…

Hi @k.kujala and welcome to the :qiime2_square: forum! [image] k.kujala: wanted to remove features with no assigned taxonomy or only assigned at the domain-level So you want to keep features like: d__Bacteria;p__Firmicutes;;;;; d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisser…

Hei, thank you for the answer. Unfortunately, it doesn't work. To give a bit more detail, before filtering I had two types of Bacteria-taxa that didn't have taxonomy assigned at the phylum level. In the phylum-level taxa barplot those were shown as 'd__Bacteria;' and 'd__Bacteria;p' The first on…

[image] k.kujala: I had two types of Bacteria-taxa that didn't have taxonomy assigned at the phylum level [image] k.kujala: 'd__Bacteria;' and 'd__Bacteria;p' The first one is indeed a feature without phylum level classification (and the command I provided to you removes them). The sec…

Hei, thanks for the explanation. I have managed to filter them by using the --p-exclude 'd__Bacteria; p__; c__; o__; f__; g__; s__' (the space after the ; is what had been missing in my previous attempts for which I had copied the taxon "name" directly from taxa barplot). As I found the assignment …

Hi again @k.kujala I'm happy you got it working! [image] k.kujala: I'm contemplating using consensus-blast instead of classify-sklearn for my whole dataset now If you want more information in order to make a decision, you may want to check this post: [image] Best Feature-C…