#pcr.seqs
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# silva.bacteria.fasta from MISeq_SOP
set.dir(input=./TestFiles, output=./TestResults/pcr.seqs, tempdefault=./TestReferences)
set.logfile(name=pcrseqs.logfile)
#trim to v4
pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F)
pcr.seqs(fasta=silva.bacteria.fasta, oligos=pcr.oligos, pdiffs=2, rdiffs=2)
pcr.seqs(fasta=silva.bacteria.fasta, oligos=pcr.oligos, pdiffs=2, rdiffs=1, checkorient=t)
quit()


