Classification performance

Hi all,

After following the Schloss SOP with some modifications for my own sample set, I got really splendid results on my subsurface water samples. I’m writing a paper on it right now (and I will not forget the citation of course), but while writing I realized I haven’t looked at the resolution of my OTU-classification. I’ve seen quite some people wonder about the percentage of sequences that were classified, e.g. to the genus level, and I actually never checked that, although it is highly important to know how much of the community I have covered in the classification part. So, is there a command in Mothur that outputs the % of sequences/OTUs that were classified to different levels (phylum, genus…) when using the classify.otu command? I couldn’t find it in the wiki, but I might have missed it, integrated in another command? Or maybe I should ‘just’ calculate this myself?



Go for it yourself :slight_smile: