Hi
I trained my own V3-V4 specific classifier using RESCRIPt from silva-138.1-ssu-nr99 and assign taxonomy using classify-sklearn but some of my features were assigned same name in family and genus level. I also tried with pretrained classifiers available in Qiime2 forum, but it also assigned the same name in family and genus level. RESCRIPt shed light on problem of missannotations in their “edit taxonomy” part. I don’t know whether this okay or I need to edit them. Can anybody suggest me what should I do or what's wrong going on here? The problem arises when I do genus level analysis after removing prefix like (f__, g__, s__) these names are suggesting family name of bacteria rather than genus name in my analysis.
| Feature ID | Taxon | confidence |
|---|---|---|
| sq3;size=70124; | d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Muribaculaceae; g__Muribaculaceae; s__uncultured_bacterium | 0.99165266 |
| sq10;size=45746; | d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Muribaculaceae; g__Muribaculaceae; s__uncultured_Bacteroidales | 0.80336385 |
| sq123;size=7619; | d__Bacteria; p__Firmicutes; c__Clostridia; o__Christensenellales; f__Christensenellaceae; g__Christensenellaceae; s__Christensenella_sp. | 0.98729090 |
| sq187;size=6953; | d__Bacteria; p__Firmicutes; c__Bacilli; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Erysipelotrichaceae; s__uncultured_bacterium | 0.99999974 |
| sq299;size=4950; | d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Tannerellaceae; g__Tannerellaceae | 0.78366247 |
| sq353;size=3729; | d__Bacteria; p__Firmicutes; c__Clostridia; o__Christensenellales; f__Christensenellaceae; g__Christensenellaceae; s__Christensenella_sp. | 0.99927360 |
| sq593;size=1526; | d__Bacteria; p__Firmicutes; c__Bacilli; o__Erysipelotrichales; f__Erysipelatoclostridiaceae; g__Erysipelatoclostridiaceae; s__uncultured_bacterium | 0.96620033 |
| sq965size=403; | d__Bacteria; p__Firmicutes; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Ruminococcaceae; s__uncultured_bacterium | 0.82221135 |
Thank you