I am using mothur to filter my shared file (made with mothur). I am using the filter.shared command and I think it works great. I understand that I need to create the OTURare to maintain the relative abundance across all OTUs. However, when I try to do taxonomic analysis, what do I do with this OTURare? should I assign it random taxa? Should I remove it? I am asking this because I need to have matching OTUs in the .shared and .taxonomy files to use the MicrobiomeAnlyst web tool. In advance, thanks for the help!
Hi Elliston - I would probably add a line to the cons.taxonomy file and give it the taxonomy of something like “Bacteria(100);Pooled(100);”
Yes, that is exactly what I did and it kind of worked. I decided I will use the Mothur tools to do the analysis and then use R to graph everything.
On that note. I am getting weird values from the
summary.single command (i.e. Simpson values higher than 1). Any idea why this might be happening?
Are you possibly using invsimpson?
Never mind, I was using the wrong file. Sorry about that.
One last question. I am comparing the alpha diversity values from the summary.single command with the ones I have calculated using the R vegan package. The Shannon and invsimpson values are the same between the 2 programs, but they are not the same for the Simpson values. Any idea why this might be happening?
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