mothur

Getting accession numbers for the identified OTUs

I’m new to MOTHUR and sorry, this might sound like a silly question: Is there any way I can get SILVA accession numbers for the identified OTUs in the final mothur OTU abundance sheet? I have a final output file (that was generated by a former group member on mothur) that has got the following info on it: “OTU ids” “Total reads” “% of Total” “Sample names” “Classification from domain up to family”. I’m now tasked with adding accession number info to this. I would really appreciate any pointers here.

your OTUs don’t have accession numbers unless you have uploaded them somewhere. Are you wanting the accession number for the closest match? that’s not how the tax id works in mothur-it uses the wang method which is a baysian method for finding the “best” id. Why do you want to do this? that can help give advice.

Many thanks for your kind response. Sorry I wasn’t very clear to you in my query: I would like to have the SILVA accession number for the closest/best match for each of the OTUs. I’ve been tasked to do this so as to compare the taxonomy of the same samples (for which 16S amplicon data has already been generated) from shotgun metagenomic sequencing. The in-house pipeline that generated the taxonomy info for the shotgun metagenomic sequencing data outputs accession numbers and the intention now is to conveniently see if there’s a match or mismatch between closest/best match taxa between what is reported through amplicon sequencing versus metagnomic sequencing. Alternatively, I’m thinking of doing a blastn against the SILVA database by using the fasta sequence file containing all the 16S OTUs predicted by mothur so as to identify the closest hit accession number. I’m aware that the bayesian method that mothur uses for classification doesn’t work like blast but from reading other posts on the forum, it does give me the impression that the results between them are mostly comparable. This way I will have a list of closest hit accession numbers to make comparisons for results between amplicon sequencing and shotgun metagenomic sequencing. What do you think about this alternative route or if there’s still a way on mothur to retrieve SILVA accession numbers for the best match, I’ll be happy to try that out too. Thank you so much again; I was lost and mere words wouldn’t suffice to express my appreciation here for you to be taking your time out to respond to my query

Why don’t you just extract the v4 16s from your shotgun sequences and run them through mothur along with amplicons?

Many thanks for your reply. I think your suggested strategy will work for me