How to change the paired-end-demux.qza into single-end-demux.qza(containing only forward reads)


I got a paired-end-demux.qza from paired reads using the following command:
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path manifest.tsv
–output-path Sr_paired_end-demux.qza
–input-format PairedEndFastqManifestPhred33V2

However, I found the reverse reads had a very low-quality scores. So I plan to use the forward reads for further analysis. Is there any method changing the paired-end-demux.qza into single-end-demux.qza containing only forward reads directly, rather than importing the forward reads again using SingleSequencesWithQuality?

Thank you!


I have good news: Yes!

Both denoising methods in QIIME 2 can accept single-end or paired-end reads… and the following methods will ignore the reverse read if it is provided:

  • qiime deblur denoise-16S (this method is intended for single-end or pre-joined reads, and so if paired-end reads are given only the forward reads are used)
  • qiime dada2 denoise-single (this method is intended for single-end reads. The separate denoise-paired method denoises paired-end reads, but denoise-single just ignores the reverse reads if they are provided)

So you do not need to do anything — just select one of the methods above for denoising and the reverse reads in your SampleData[PairedEndSequencesWithQuality] artifact will be silently ignored.

Good luck!

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Good news to me. Thank you!