How to denoise pair end reads only using the forward read as my amplicons don't overlap.

Hi there,

I am running paired end sequencing of the conserved adenylation domain of NRP type gene clusters. Due to the mixed orientation issue I am needing to import my data to Qiime as paired end so I can run qiime cutadapt demux-paired with --p-mixed-orientation enabled.

However when I get to denoising I only want to analyse the forward read becuase the amplicons for this do not overlap. How would I go about doing this?

Hi @Lamm-a,

You can simply take the output from your qiime cutadapt demux-paired ... command, in which the output file is of the type SampleData[PairedEndSequencesWithQuality].

This is one of the allowed types you can use for input into the qiime dada2 denoise-single ... command, as it is smart enough to only denoise the forward reads from the paired-end output.