Good Day Forum,
I’m using the stability.batch file as a tempate for my batch code. I don’t have a Mock sample in my analysis and would like to know which code(s) I need to remove from the stability.batch file so I can run it without a Mock group. Could someone help assist? Thanks!
pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F)
system(mv silva.bacteria.pcr.fasta silva.v4.fasta)
#change the name of the file from stability.files to whatever suits your study
make.contigs(file=stability.files, processors=8)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=silva.v4.fasta)
screen.seqs(fasta=current, count=current, start=1968, end=11550, maxhomop=8)
filter.seqs(fasta=current, vertical=T, trump=.)
unique.seqs(fasta=current, count=current)
pre.cluster(fasta=current, count=current, diffs=2)
chimera.uchime(fasta=current, count=current, dereplicate=t)
remove.seqs(fasta=current, accnos=current)
classify.seqs(fasta=current, count=current, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)
remove.groups(count=current, fasta=current, taxonomy=current, groups=Mock)
cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.15)
make.shared(list=current, count=current, label=0.03)
classify.otu(list=current, count=current, taxonomy=current, label=0.03)
phylotype(taxonomy=current)
make.shared(list=current, count=current, label=1)
classify.otu(list=current, count=current, taxonomy=current, label=1)