consensus.seqs input files

Commands in mothur
1

Hi,
I’m having some problems with consensus.seqs. I’m following the Schloss SOP and after classify.otu I would like to get a list of consensus sequences for my OTUs. I use the command:

consensus.seqs(fasta=merged.shhh.trim.unique.good.align, list=final.an.list, label=0.03) or
consensus.seqs(fasta=final.fasta, list=final.an.list, label=0.03)

With the fasta either being the initial alignment or the ‘final’ fasta after removal of contaminants.

Either way I get an error stating that specific seq names are not in the fasta, suggesting that the list file still contains seq names that have been sorted from the fasta file. When using the original fasta file before alignment I get an error because sequences are not of the same length. Am I using a wrong list or fasta file or what seems to be the problem?

Any suggestions are much welcome!

Sincerely, Sandra

2

You need the names file

3

Thanks, that did the trick.

Maybe a very trivial question, but is there a quick way to get the consensus seqs without the gaps for easy BLAST?

Thanks again !

4

The degap.seqs command will remove the gaps for you, http://www.mothur.org/wiki/Degap.seqs.

5

I cannot say this too many times:

Thank you again for an amazing program and support forum!!!

Sandra