quality-filter q-score on joined demux ignoring reverse reads

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Hello,

I am trying to quality filter illumina data that I've imported via a manifest file for DADA2 denoising. The import (type SampleData[PairedEndSequencesWithQuality]) went well, no issues, summary looks good.

Basically, I'd just like to tell DADA2 to cut off (exclude) base reads below a certain quality score threshold. I'm not as concerned as actual positions are concerned.

When I tried this with my demux paired qza using quality-filter q-score, the filtered sequences output qza only had filtered data for the forward reads. No reverse reads were present.

If anyone has any info about this tool, or ways of fine-tuning quality control before or during denoising, I'd greatly appreciate it!

Many thanks,
Elliot

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Hello @prophet18,

You can use the --p-trunc-q parameter to dada2. See here for a description of all the ways to tweak denoising using dada2.

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