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

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)

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

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

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