should remove unassigned genera in 16S rRNA sequencing analysis

Question

[zhangdengwei]

Hi all,

When analyzing 16S rRNA amplicon data from tissue samples, I found some ASVs could not be taxonomically assigned at the genus level. Rather they can be assigned at a higher level. I wonder whether I should remove those ASVs for downstream analysis if I use genus data, or group them into others. I did not find any paper stating this issue specifically. Any suggestions would be greatly appreciated.

[andres.firrincieli]

You should not remove those ASV. Rather, use tax_fix() from microViz to fix the taxonomy table.

[zhangdengwei]

Hi @andres.firrincieli, I agree with you that those ASVs should not be removed. However, the abundant genera shown in many papers did not include any uncultured or unknown genera, I wonder whether they have removed that information when comparing. Besides, I also found someone indeed removed those ASVs (e.g. https://www.thelancet.com/action/showPdf?pii=S2352-3964%2823%2900260-8).