I removed Eukaryota from my samples since I had a lot of host DNA. However, what happens is that when you make the taxa bar plot, you can see that those sequences were not removed and just moved to unassigned sequences. Otherwise, why wouldn’t the relative abundances change?
How did you remove the Eukaryota? Could you walk me through the steps/commands?
Yes, here is the code I used:
Remove Euakaryota from the feature table
qiime taxa filter-table
Make taxa plot without the Eukaryota
qiime taxa barplot
@Negin, it sounds like you were able to resolve your filtering issue on this other thread (linked below), but please let us know if you are still having issues related to filtering unclassified/eukarya.
I tried Greengenes, it gave me completely different taxa results. V4 primer-trained classifier was worse so I just used the pre-trained classifiers from QIIME2 website. I was able to remove Eukaryota as well as Unclassified but I can’t seem to be able to get rid of D-0-Bacteria;-;-;-;-;-. I tried different methods. None of them worked. Any hints?
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