Summary taxonomy table from filtered .shared file

Hi,

I have a consensus taxonomy-file of my OTUs (from classify.otu command) and a .shared-file that was filtered (filter.shared) to remove some rare OTUs.

What command should I use to make a summary taxonomy table (rows are taxons and columns are samples) of the filtered .shared file? Is it possible? If it not possible, could it be possible in the future?

And another thing.

I noticed that this article (Dumont et al. 2014)

has published a mothur-compatible classification database of pmoA-gene. Perhaps it (or at least the reference) could be added to taxonomic database download page in mothur wiki?

Best,

Antti Rissanen
Jyvaskyla University
Finland

If you run classify.otu on the list file that is used to make the shared file then the OTUs will align. The OTU labeling is preserved after subsampling.

I noticed that this article (Dumont et al. 2014)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927136/

has published a mothur-compatible classification database of pmoA-gene. Perhaps it (or at least the reference) could be added to taxonomic database download page in mothur wiki?

It’s a wiki - go for it! :slight_smile:

Now I did not understood. Sorry.

Yes, I have a list file but it was generated before I filtered my .shared-file to remove rare OTUs.

I also have consensus taxonomy of OTUs because I already ran classify.otu on the whole non-filtered data.

If I now ran a classify.otu with the list file it will give summary taxonomy table of the non filtered data, and I already did that. I would like to have the summary taxonomy for the filtered data. Should I have a list file of filtered shared file to be able to do this?

It might also be that I am not thinking clear enough now. Too much mothur?

Best,

Antti

After going through mothur manual, I noticed a command remove.rare.

Good.

That solves my problem. I can remove the rare OTUs already from the list-file and then proceed.

Thanks,

Antti