iontorrent split regions

hi

I’m trying to split Iontorrent fastq files by region.
I know the f,r primer information.

Should I use both --p-front and --p-adapter?

Why did you only use --p-front here?

Thank you.

Hi @kimshinseung,

When you trim the regions, you want them to all start at the same place. So, --p-front will make sure that you trim anything before that primer sequence. That way, all your sequences are aligned in the same place, and your ASVs will be comparable.

Best,
Justine

Thank you very much for the answer.

I tried to divide it into 7 variable regions using cutadapt.

I created and merged 2 v2f,v2r files.

Likewise for v3,v4…, f,r were created and merged using each primer.

Is the way right?

Thank you.

Hi @kimshinseung,

It depends on what your reads look like. Do you have paired reads or single end reads? I thought Ion Torent gave you only forward reads.

Best,
Justine

iontorrent is single ended, f and r are mixed.

Is the method I presented valid?

I wonder if there is a better way.

Thank you.

Hi @kimshinseung,

I’m sorry for the delay on this!

Yes, the plan to split your reads makes sense to me. They’re all imported single end, and then you’ll separate them by trimming with the forward and reverse primers.

Best,
Justine

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