Hello again.
I’m working with my 454 pyrosequencing environmental samples from soil following Schloss SOP.
I have run all first commands, except for the ones designed to “remove contaminants”.
Due to the kind and the conditions of my sampling site, I am specting a high number of Cyanobacteria-class OTUs, but I have a little number or directly I don’t get any.
Is it possible that I have removed them with any of the steps before?
I attach the Batch file I am using:
unique.seqs(fasta=xxxxx.trim.fasta)
align.seqs(reference=silva.bacteria.fasta)
screen.seqs(start=1044, optimize=end, criteria=95, minlength=250)
filter.seqs(vertical=T, trump=.)
unique.seqs()
pre.cluster(diffs=4)
chimera.uchime()
remove.seqs()
summary.seqs()
split.abund(cutoff=2)
dist.seqs(fasta=xxxxx.trim.unique.good.filter.unique.precluster.abund.fasta)
cluster(name=xxxxx.trim.unique.good.filter.unique.precluster.abund.names, method=furthest)
get.oturep()
Thank you very much