Hello,
I've been using QIIME and Mothur to analyse different sets of 454 data, and this is a little off topic, because it's related to Sanger data... still I think my problem can also happen with NGS data.
So, I have Sanger generated data for a functional gene and I want to use Mothur to acess the existance of OTU's...(i.e create a distance matrix and cluster, according to a given cutoff).
I produced an alignment in fasta format, created the phylip distance matrix (column formatted) using the dist.seqs command, as follows:
dist.seqs(fasta=aligned.fas, output=squared)
then I clustered using the cluster command, as follows:
cluster(phylip=aligned.square.dist, cutoff=0.05)
Hence, the list file should give me a list of the existing OTU's at different levels, but I only get those that are unique, 0.01, 0.02 and 0.05... and I'd like have information regarding the 0.03 cutoff, because I want to compare the clusters I get with a 0.02 and 0.03 cutoff (98% and 97% respectively).
I've tried to set the cutoff to 0.04, 0.03, I've played with the "hard=t" and the "precision" options, and I still can't figure this out... can someone help me with this, please?
I've been using QIIME and Mothur to analyse different sets of 454 data, and this is a little off topic, because it's related to Sanger data... still I think my problem can also happen with NGS data.
So, I have Sanger generated data for a functional gene and I want to use Mothur to acess the existance of OTU's...(i.e create a distance matrix and cluster, according to a given cutoff).
I produced an alignment in fasta format, created the phylip distance matrix (column formatted) using the dist.seqs command, as follows:
dist.seqs(fasta=aligned.fas, output=squared)
then I clustered using the cluster command, as follows:
cluster(phylip=aligned.square.dist, cutoff=0.05)
Hence, the list file should give me a list of the existing OTU's at different levels, but I only get those that are unique, 0.01, 0.02 and 0.05... and I'd like have information regarding the 0.03 cutoff, because I want to compare the clusters I get with a 0.02 and 0.03 cutoff (98% and 97% respectively).
I've tried to set the cutoff to 0.04, 0.03, I've played with the "hard=t" and the "precision" options, and I still can't figure this out... can someone help me with this, please?