Hello! Thank you all for your previous help.
So Ive got quite far in my pipeline, but now I’m stuck as to how to assign my samples to treatment groups?
Here are the scripts I’ve ran so far:
BATCHI
mothur “#set.dir(input=/scratch/micro/nb326/temp_bpsenvs/01_rawdata, output=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess); make.file(inputdir=/scratch/micro/nb326/temp_bpsenvs/01_rawdata, type=gz, prefix=tbps); make.contigs(file=current, oligos=/scratch/micro/nb326/temp_bpsenvs/01_rawdata/abps.oligos, pdiffs=1); summary.seqs(fasta=current)”
BATCHII
mothur “#set.dir(output=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess); screen.seqs(fasta=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/tbps.trim.contigs.fasta, group=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/tbps.contigs.groups, summary=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/tbps.trim.contigs.summary,maxambig=0, minlength=252, maxlength=254, maxhomop=8); summary.seqs(fasta=current); unique.seqs(fasta=current); count.seqs(name=current,group=current);summary.seqs(fasta=current,count=current); align.seqs(fasta=current,reference=/home/n/nb326/miniconda3/envs/bpsenv/silva/silva.nr_v138/silva.nr_v138.align); summary.seqs(fasta=current,count=current)”
Batch III
mothur “#set.dir(input=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess, output=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/trains); screen.seqs(fasta=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/tbps.trim.contigs.good.unique.align, count=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/tbps.trim.contigs.good.count_table, start=13862, end=23444, maxhomop=8); summary.seqs(fasta=current, count=current); 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); summary.seqs(fasta=current, count=current)”
Then I changed the names of the final output fasta and count file generated in this batch job to tbps.train.fasta and tbps.train.count.
BATCH IV
mothur “#set.dir(output=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/trains); classify.seqs(fasta=home/n/nb326/miniconda3/envs/tbatch/03_preprocess/trains/tbps.train.fasta,count=/home/n/nb326/miniconda3/envs/tbatch/03_preprocess/trains/tbps.train.count_table,reference=/home/n/nb326/miniconda3/envs/tbatch/trainset18_062020.rdp/trainset18_062020.rdp.fasta,taxonomy=/home/n/nb326/miniconda3/envs/tbatch/trainset18_062020.rdp/trainset18_062020.rdp.tax, cutoff=80); remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-Eukaryota); remove.groups(count=current, fasta=current, taxonomy=current, groups=SAM1.raw-SAM3.raw)”
Right now I have 96 groups. I have 96 samples I sent for sequencing. If I want to add these samples to treatment groups, to do unifraq analysis what do i do please?
Thanks in advance!