can anyone help me as i have analyzed my 16Sr RNA (v3-v4 region) in qiime2 with SILVA database.
I am getting 60 assigned phyla, around 700 assigned genera however, very few assigned species (132/171). Is this possible ? or there is some problem . i think assigned species should be greater than assigned genera.
please help me with this.
I think, it is quite common for 16S amplicon sequencing.
Although it seems to be logical, the problem is that resolution of 16S amplicons often are too low to assign species since you are targeting only 1-2 hypervariable regions. So most of the reads are assigned only to the genus level.
And a lot of researchers prefer to work with 16S amplicons only at genus level, since species annotations are not so reliable with it.
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