Question: Classify 16S Reads
0
gravatar for sebabiokr
4.0 years ago by
sebabiokr10
sebabiokr10 wrote:

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 thare any way to reduce/improve the unclassified reads?

Thank you

Sebastian

amplicon 16s • 1.4k views
ADD COMMENTlink modified 2.1 years ago by Josh Herr5.4k • written 4.0 years ago by sebabiokr10

> is thare any way to reduce/improve the unclassified reads?

The short answer: No.  

We need better databases.

ADD REPLYlink written 2.1 years ago by Josh Herr5.4k
1
gravatar for cts
4.0 years ago by
cts1.5k
Pasadena
cts1.5k wrote:

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

ADD COMMENTlink written 4.0 years ago by cts1.5k
0
gravatar for Manu Prestat
4.0 years ago by
Manu Prestat3.8k
Marseille, France
Manu Prestat3.8k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Manu Prestat3.8k

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

ADD REPLYlink written 4.0 years ago by sebabiokr10
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