I have an artifact with the type SequenceData[PairedEndSequencesWithQuality]. I have already removed the adapters. I want to filter it with quality-filter then use dada2. The two methods in quality-filter return “sequences with quality” or “joined sequences with quality”. I cannot find a way to do this (due to artifact type compatibility)
This is intentional — dada2 does not accept joined sequences because (1) the dada2
denoise-paired method joins the reads for you after denoising each one and (2) joining the reads can wreck the Q scores (some joiners just give the overlapping bases arbitrarily high Q scores) and this conflicts with the error profiling that dada2 performs.
So just use your
SequenceData[PairedEndSequencesWithQuality] as input to dada2.
This is not necessary, since dada2 already does an initial pass for low-quality sequences (see the
max-ee parameter), which is why that method has not be set up to accept paired-end reads.
I hope that helps!
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