Hi. I’m new to Qiiime, still trying to learn how to use it.
With our set or primers, there is a full overlap between forward and reverse reads and we already receive the samples demultiplexed.
I was able to import my data into Qiime2 using Casava 1.8 paired-end demultiplexed fastq importing function (qiime tools import \ --type ‘SampleData[PairedEndSequencesWithQuality]’ ). After doing this, I realized that the quality of my reverse reads are not good.
So, I’m wondering, considering the full overlap between my F and R reads, can I disregard my reverse reads and only import my forward reads using qiime tools import \ --type ‘SampleData[SequencesWithQuality]’ ?
Would this approach be correct? Will my results using both approaches be quite different from each other?
You can absolutely do this, and it’s something we often recommend if merging isn’t working or the reverse reads are junk. If you have a real biological signal, you should see consistent results.
In fact you don’t even need to re-import your data, qiime dada2 denoise-single accepts SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] which means you can supply either to it. When you give denoise-single paired-end data, it will just use the forward reads.