screen.seqs maxlength

Commands in mothur
1

Dear all,
thanks for this forum,

I have a question concerning the screen.seqs option maxlength.
I am following the MIseq sop http://www.mothur.org/wiki/MiSeq_SOP, regarding the command line

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, summary=stability.trim.contigs.summary, maxambig=0, maxlength=275)

How do you figure out the maxlength.


Best reagards,
2

You would need to use a reference database and trim it to the region that you are interested in. Then see what variation you have in your sequence length. In general, it’s hard to argue for a 16S rRNA gene region other than V4 (http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/)