Import both forward and reverse reads or only forward reads?

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?

Thanks in advance,
Fernando Studart

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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.

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Hi Evan,

Thanks for your reply and support.

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