output of tables-genus.qza

General Discussion
#1

Hi, thank you guys in advance!

Does anyone know the difference between k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;__andk__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__?

Are they the data of two families f__Erysipelotrichaceae which can’t be identified the specific genus?

Many thanks,
Jiqiu

#2

Hi @Jiqiu,

Welcome to the :qiime2: forum!

Is a specific family that is unnamed/unclassified in Greengenes itself.

I think

means that the classifier couldn’t define it past the family level.

…I tend to do some manual clean up and when I do, I often use ‘unspecified’ or “uncultured” for the g__ taxonomy (“unspecified family Erysipelotrichaceae”) and “unclassified” for the second when I present the results, as much as a note to myself as anything else.

Best,
Justine

#3

Thanks for you reply!

But i consider if what you said is true, the count number of first line should be larger than the number of the second. Right?

But in my data, i can’t observe this.

Many thanks,
Jiqiu

#4

Hi @Jiqiu,

What do your confidence values look like? How did you assign taxonomy?

Best,
Justine