Question: Identify OTU to species by using MOTHUR
gravatar for liqing1123
2.1 years ago by
liqing11230 wrote:

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}/, cutoff=70);

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