Classify problems (classification non replicable)

Commands in mothur
1

Hi

I am working with pyrosequences of 16S. I tried to classify it using classify.seqs with the SILVA database provided by your site. The first time the output shown me that more than 60% of 12 independent libraries were Bacteroidetes, I founded this suspect. Today I run the same libraries again and now the output said that around 50% of the sequences are Acidobacteria :o I do not know why the classification are not consistent, Which could be the problem?

I use the default options
classify.seqs (fasta=S1_T_3.fasta, template=nogap.bacteria.fasta, taxonomy=silva.bacteria.silva.tax)

My fasta files are not aligned…

I am confuse about this, could you help me please?

Esme

2

It’s hard to say without seeing the input you used to both runs of classify.seqs. We have no problem with reproducibility on our end. If you can reproduce this behavior we’ll happily take a look at it for you.

Pat

3

Hi

I think that I know what happens!!!

If I do the analysis of different libraries in the same folder and don’t erase the out files of the first library, apparently mothur use these files and gave me different results. Is this possible?

Esme