I am a new Qiime 2 user and I am attempting to import joined fastq files (this means that I have only one fastq per sample that includes R1+R2 joined). I am not sure how to import it into Qiime 2 in order to do quality filtering with DADA2.
Ideally you would import them unjoined, and allow DADA2 to do QC on both directions before merging. This thread has some good discussion on why you’d be better off doing that.
If that isn’t possible, you could probably treat them as single-end so long as your read-joiner produces “good” quality scores for the overlapped region between R1 and R2 (see linked thread for discussion), you could use
If that also isn’t the case,
deblur should work fine on your merged reads, as it works in a different way.
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The QIIME 2 2017.11 release has expanded support for analyzing paired end reads! See the paired end reads community tutorial for more details.