I need to merge demultiplexed paired-end reads to a single fastq file for each sample for uploading to a repository. Is there a way to obtain these files from QIIME2, rather than using a completely separate tool like FLASh?
I checked the demux-paired-end.qza file and there is still a R1 and R2 file for every sample, so I assume that they aren’t merged?
Thanks in advance!
Hi, @kms285! Welcome to the forum.
If I understand correctly, the following workflow should get you what you need:
First, use the
join-pairs method to merge your paired-end data:
qiime vsearch join-pairs \
--i-demultiplexed-seqs demux.qza \
This will generate an
SampleData[JoinedSequencesWithQuality] artifact, which you can then export:
qiime tools export \
--input-path joined.qza \
If you take a look in the resulting directory you will find a single fastq for each of your samples.
This worked perfectly! Thank you!
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