Classify 16S Reads

Question

[sebabiokr]

Hello, I have classified 16S rRNA metagenomic reads against RDP and SSU reference database. more than 30% reads classified as unclassified (derived from bacteria).

Is there any way to reduce/improve the unclassified reads?

Thank you

Sebastian

[Josh Herr]

Is there any way to reduce/improve the unclassified reads?

The short answer: No. We need better databases.

Answer 1

[cts]

You could try a different database. RDP does not include environmental clusters, which can be a substantial proportion of amplicons. Perhaps see if you get more classification when using GreenGenes or SILVA

Answer 2

[Manu Prestat]

It sounds to me pretty reasonable, depending on where your samples are from (there is more unknown in prairie soil that mammal gut for instance). If your data are sequenced amplicons like I suspect, did you "denoise" and filter chimera as a preliminary step? It should help.

[sebabiokr]

Yes its 16s Specific amplicons from fecal samples. i used mothur, QIIME for denoising and chimera checking. Dataset confirmed no chimeras. Thank you