I am following MiSeq_SOP to do some test on mothur commands for future analyses and I have found some problems with it for what I want to do later with my own sequences.
The last step I have made is clustering the sequences into OTUs with
And after that, I got a .shared file with
Now I want to do 2 things:
First, I have to subsample my groups to rarefy the sequences in each group.
Second, I need to assign the taxonomy to the sequences.
I do not know which action would be better to do first, but anyway, what I want to do is to assign the taxonomy with a different database than the SILVA one, specifically, with RDP.
To do so, I have downloaded the unaligned Bacteria 16S fasta file from its webpage, but as I see, a .tax file is needed to complete both the classify.seqs and the classify.out commands, and I do not know where to get it or how to generate it for the RDP.fasta I have.
Does anyone know how to get a .tax file that couples with the RDP.fasta file?
If it is not possible to do this, I have thought of getting the OTUs representative sequences that could come out from the ‘’‘cluster’’’ command to campare it outside mothur (maybe on RDP classifier).
For doing that, I have thought of using
probably with the options
column=, list=, count=
Would it be correct to do that? Is any other way to get the representative sequences that would be included in the .shared file?
Thanks a lot