get.oturep: no fasta file?

Commands in mothur
1

Hi,
I’m running the get.oturep command and only seem to be getting .names files out of it and no fasta file. From the wiki I got the impression that I should get both: ‘A .rep.fasta and .rep.names file is generated for each OTU definition’
What I’m looking for is a representative sequence for a specific OTU.

Any suggestions?
Thank you! Sandra


I've followed the Schloss SOP; dist.seqs, cluster, etc and classified the OTUs. Summary of the run is here:

mothur > get.oturep(column=final.dist, name=final.names, list=final.an.list)

********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||

unique 4046
0.01 3321
0.02 2033
0.03 1322
0.04 974
0.05 781

Output File Names:
final.an.unique.rep.names
final.an.0.01.rep.names
final.an.0.02.rep.names
final.an.0.03.rep.names
final.an.0.04.rep.names
final.an.0.05.rep.names

2

I confirm, no fasta formatted file are returned.

3

Hi Cris,
But do ou know how to get the sequence then, I find the final.an.unique.rep.names confusing as the sequence IDs do not appear to represent the OTUs but rather the unique sequences (more rep. IDs than OTUs)?
Thanks, Sandra

4

You must include the fasta file in the command: get.oturep(column=final.dist, name=final.names, list=final.an.list, fasta=final.fasta).

5

ah, great. Thank you!