Imprecise taxon classification...but only in one group!

I've just completed my first QIIME-based analysis, looking at COI in fox scat. The results look plausible, but for one thing: a very high proportion of ASVs are classified simply as "Actinopterygii," with no taxonomic resolution below the level of class. This does not occur in other groups (e.g., invertebrates are well differentiated the level of genus and species). Before posting all the commands I used, I just want to get a sense for whether this is a frequently-encountered phenomenon with a known cause. Could it be a filtering issue? In which case, why only bony fishes? I'm using a whole-database download of BOLD in my feature classifier, and it's got plenty of well-annotated fish sequences. As for version: I'm running QIIME2-2022-11 in a conda environment under POP! OS, on a System76 Linux laptop.

Hi @skaup ,

Welcome to the forum! I think I know what is going wrong. This sounds quite similar to this topic:

The issue is most likely that the database you built contains one or more of:

  1. very short sequences that skew classification
  2. misannotated sequences

How did you build your classifier? You can use the plugin RESCRIPt to visualize the length distribution and filter your sequences by length to remove any outliers that are causing possible issue #1. See also the topic I shared above (and the posts linked therein) for some more troubleshooting.

The issue is probably not with bony fishes per se, but that there are 1 or more reference sequences that are really short and/or misannotated as bony fishes. Hence you have a very high number of query sequences being classified as Actinopterygii. So the ASVs are either being misclassified as Actinopterygii, or matching a reference sequence that is misclassified as Actinopterygii.

I suggest filtering/looking at the length distribution first to see if this already improves your results... if not, you should see if there are any reference sequences that are only classified at the class level.

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