I get too many OTUs. Like almost same as sequence number.

Commands in mothur
1

Dear All,

When I run this commands below I get too many OTUs, which will not help me. I get almots as much as OTU number as my sequence number. I try this but couldn’t get any further please help me.

  1. trim.seqs(fasta=x.fasta,oligos=x.oligos,allfiles=t,processors=8)
  2. unique.seqs(fasta=x.fasta)
  3. align.seqs(candidate=x.unique.fasta,template=silva.bacteria.fasta,flip=t,processors=8)
  4. filter.seqs(fasta=x.unique.align)
  5. dist.seqs(fasta=x.unique.filter.fasta,calc=onegap,countends=F,cutoff=0.03,output=lt,processors=8)
  6. cluster(phylip=x.unique.filter.phylip.dist,name=x.names,method=furthest,cutoff=0.03)
  7. classify.seqs(fasta=x.fasta,template=nogap.bacteria.fasta,taxonomy=silva.bacteria.rdp6.tax,cutoff=60)
  8. classify.otu(taxonomy=x.rdp6.taxonomy,list=x.unique.filter.phylip.fn.list,label=0.03)
2

What kind of sequences (target and sequencing kit version)?

3

16s is the target and using standard Illumina procedure for sequencing

4

What region and what version of the chemistry are you using. You likely want to be familiar with this…

http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix/