MOTHUR: screen.seqs option "maxlength" & "minlength"
Entering edit mode
16 months ago
dpc ▴ 210

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

16s mothur metagenome microbiome • 436 views

Login before adding your answer.

Traffic: 2473 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6