mothur

ITS2 screen.seqs

Hi,

I am working with ITS2 sequence data and looking around the group for ITS2 sequence data but I did not find a good answer for me. I am keen on discussing how could I choose the screen.seqs: minlength and maxlength. Please see the summary.seqs below.

image

I have tried:
screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, minlength=290, maxlength=480)

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=480)
Many thanks.

Cheers

Hi there,

I suspect you used 2x300 nt reads? If that’s the case, then I’d be reluctant to use anything much shorter than 300 nt and anything around 600 nt is likely garbage that didn’t actually assemble. I suspect you could also safely use maxhomop=10

Pat

Hi Pat, Great, many thanks for your suggestion. That’s right I had 300PE reads. I will try to use maxhomop=10 then inform you.

Cheers,
Truong

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.