Entering edit mode
6.9 years ago
liqing1123
▴
10
Dear All, I used Mothur to do the 16S analysis and I have encountered to one problem: I cannot annotate my OTUs to Species, the highest taxa I was able to reach is Genus. I have use the SILVE databases and the command as following. Has anyone give me some suggestions to annote the sequences to speices? I know that this may be feasiable with GreenGene database and QIIME, but I would like to keep the use of Mothur since I have built the process with Mothur.
Mothur classify.seqs(fasta=current, count=current, reference=${SILVA_HOME}/trainset9_032012.pds.fasta, taxonomy=${SILVA_HOME}/trainset9_032012.pds.tax, cutoff=70);
Dear liqing123 I am managing the same issue: SILVA db seems to not have species level at all. It is not a setting failure of your code. Now I will try to use GreenGene on the same Mothur pipeline.
With just one phylogenetic marker (16S rDNA) is very hard to classify down to specie level. This has nothing to do with the databases SILVA/greengene or the pipeline QIIME/Mothur.
Thank you for your specification for me and for the original post. You are introducing the reliability issue of species level (only with 16S) identification. Anyway still remains the technical fact that SILVA has not species level at all: reliable or not it can't have species level in output. GreenGene goes better on this point, because seems to have a 10% coverage at species level.
Just my personal opinion; you are choosing a database based on a feature that is completely useless in regard to the 16S rDNA analysis. Also, keep in mind that greengene is no longer supported since 2013.