ITS2 screen.seqs

Commands in mothur
1

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

2

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

3

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

4

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