how to generate a fasta file of all sequences in an otu?

Commands in mothur
1

Hi,

How can I generate a fasta file with all sequences assigned to a given otu?

The file I have is an *.an.list, generated at the stage:
mothur>cluster.split(fasta=final.fasta, taxonomy=final.taxonomy, name=final.names, taxlevel=6, processors=2)

We have a large set of 250nt long sequences of a variable region of the 16S gene in the first otu0001 at the 0.01 difference level,
and we would like to run unique.seqs on the obtained fasta file to check the precise taxonomic affiliation best hit of the different unique sequences in the otu.

Thanks in advance,
Stéphane

2

myLabels.txt contains the OTU labels you are interested in. Here’s the commands you would run:

get.otulabels(list=final.an.list, label=0.01, accnos=myLabels.txt) - select the OTU’s from the list file you are interested in
list.seqs(list=current) - list sequences in the OTUs
get.seqs(fasta=final.fasta, name=final.names, taxonomy=final.taxonomy) - selected sequences from the fasta, names and taxonomy files.

3

Hello,
thank you very much for your fast answer, will try that asap!
Best,
S