Reference Database(s) for 18S

Theory behind mothur
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Hello again (apologies for so many posts lately),

To analyze18S v9 sequences, I have made a few substitutions for reference sets. For instance, I am using silva.nr_v132 instead of silva.seed

I also used trainsets16_022106.pds instead of trainset16_022016.rdp side question, why switch from silva to rdp at this point in the analysis?)

After running ‘classify.otu’, however, almost all levels of the taxa have shown up as ‘Eukaryota_Unclassified’. Could this be due to the reference datasets I have used not containing enough 18s sequences?

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The RDP trainset database only has a minum number of 18S rRNA gene sequences to be able to classify things as Eukaryotes or not. I would encourage you to use the silva reference database for alignment and classification

Pat

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