mothur

Trim.seqs issue with ITS

#1

Good day,

I am having an issue with the trim.seqs command in an ITS workflow. I do not have an oligos file to work with, because the people at my sequencing facility have already trimmed the primers and barcodes from my sequences. So what I’m trying to do is use the trim.seqs function with the maxlength as my parameter. At first, I set the maxlength to 250. The command ran, but when I tried to run my summary table I got an error due to missing values. I then ran trim.seqs again, but this time with a maxlength of 300 basepairs. This time the summary.seqs command for my output worked, but it DRASTICALLY reduced my number of sequences to a point that I think it wrong.
Here is my summary.seqs for the output of my screen.seqs function: Image 10-5-20 at 5.27 PM

And here is the summary.seqs for the output of my trim.seqs after I have set the maxlength to 300 basepairs:
Image 10-5-20 at 5.29 PM

I would dearly appreciate any advice about how to proceed with this trim.seqs command.

All the best
Nicolas

#2

Hi - I’m pretty sure trim.seqs is working like screen.seqs would when given maxlength. Can you try using keepfirst=300 in trim.seqs if you only want the first 300 nt?

pat

#3

Hi Pat. Thanks for your response. I don’t necessarily want to only keep the first 300 nt. I just want to make sure that my sequences are quality-trimmed. I skipped this step previously and ended up with way too many OTU’s in my .shared file. So basically I’m just screening my data in a range that makes sense, based on what the sequence freq histogram looks like on Genious.

#4

I guess I’m not sure what you’re trying to do. If you’re doing it based on quality scores, you could do it with one of the other options in trim.seqs