Regarding taxonomy profiling outcome using silva138_AB_V3-V4_classifier.qza classifier

I am running qiime2-2023.5 version and used silva138_AB_V3-V4_classifier.qza classifier fro toxonomy classification. When I visualized .qzv file, I observed higher "d__Bacteria;;;;;__". I am concerned if the outcome is true or due to any error. I haved attached csv file fro your reference.
level-6.csv (202.4 KB)

Hi @laxmi_sharma
I often find in my data that this is a true signal. In my data its typically non bacterial contamination that the classifier is labeling as bacteria because the classifier has a limited knowlegde.

The way I test this :mag: is I look at the rep-seq.qzv and blast the sequences that are labeled d__Bacteria. If these come up as not bacterial then its probably non bacterial contamination and should be filtered out.

If they come back as actual bacterial sequences then it might be an issue upstream.

Hope that helps!


Thank you @cherman2 for the information.
I have one more question regarding classier use. Can I use full length 16S rRNA classifier irrespective of samples 16S rRNA hypervariable region? I am trying to analyze publicly available 16S rRNA sequences.

Hi @laxmi_sharma,

This should work for getting a consistent taxonomy!

Thanks @cherman2 for getting back to me.