Hello friends!!! My query is regarding the "screen.seqs" command that is used before the alignment step ("align.seqs") in mothur software. I’m confused about what value to use for maxlength and minlength options. Thus I was thinking of avoiding the “screen.seqs” step before alignment. Can I just avoid “screen.seqs” command before alignment and go to the alignment step with all of my sequences and remove sequences with ambiguous bases after the alignment? I want to follow this workflow:
make.file(inputdir=./MiSeqSOP, type=fastq, prefix=stability) make.contigs(file=current, processors=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=silva.v4.fasta) summary.seqs(fasta=current, count=current) screen.seqs(fasta=current, count=current, start=1968, end=11550, maxhomop=8, maxambig=0) summary.seqs(fasta=current, count=current) . . .
thanks & regards, DC7