Identifying the OTU ID for a particular taxa

[Mei San Tang]

Hi,

I've identified a taxon that I'm interested in based on my LEfSe analysis. The taxon is named

k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Prevotellaceae.g__Prevotella on my L2 OTU table (of which I generated from taxa summary). I wanted to identify the OTU ID of this taxon in order to obtain its representative sequence set. However, when I referred back to my heat map, I realized that there were several taxa with the same name but different OTU ID. I'm not sure as to which OTU ID I should be selecting. I've tried removing singletons by running the filter_otus_from_otu_table.py, but it didn't help as the situation remained the same - I still ended up with equal number of OTUs named under this taxon. Should I be increasing the counts per OTU, filter low abundance OTU (of which I'm a little hesitant since my interest in this taxa isn't really driven by abundance) or should I just pick all the OTUs under this taxa?  Also, I realized that many taxa names appearing in the heat map isn't included in the taxa summary, why is this happening? Thanks, Meisan

[Laura Wegener Parfrey]

Hi Meisan,
Whether you want all of the Prevotella sequences or only one depends on the downstream analysis you want to do.  If you want just one sequence you most likely do want to choose the OTU with highest abundance.  There are many ways to determine the one with the highest abundance but the easiest is probably to convert your otu table to classic format with convert_biom.py  (you should specify these options as well as in and out files:  -biom_table_type="otu table" --process_obs_metadata taxonomy -b --header_key taxonomy )

Then you can open the classic OTU table in excel, sum OTU abundance, and choose your most abundant Prevotella.

Laura

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Laura Wegener Parfrey
Postdoctoral Research Associate
University of Colorado
Boulder, CO 80309

[Mei San Tang]

Hi Laura,

Thanks for the suggestion. It works for me.

Meisan