Re-analyzing QIIME1 demultiplexed paired end reads on QIIME2 and missing barcodes.fastq.gz file

Hey guys,

I am pretty new to QIIME2 but i went through the tutorials successfully. I have some 22 QIIME1 paired end fastq files that I wanted to re-analyze using QIIME2.

First stumbling block is that the paired end reads seem to already have been demultiplexed as each set of paired ends correspond to specific samples. How do I undo that step using QIIME2 if possible? and have one pair of paired end reads to represent all samples for QIIME2. I no longer have QIIME1 on my system but I can always re-install it if I need to use it.

Next problem, how do I create the barcodes.fastq.gz file?

I would be happy for any help on this.

Hey there @dawkinsk2014!

Is there any particular reason you want to re-multiplex your reads? Personally, if my data was already demuxed, I would want to import and start working from there!

We have some very relevant documentation for you here in the Importing Tutorial - please take a look and lets us know how it goes! :qiime2: :t_rex:

Hey Matthew,

Thanks for responding. I will check out that tutorial.

I wanted to re-multiplex because all my samples are in separate fastq files and I wanted to get them back to one set of paired end fastq files to be used in QIIME2. And I wasn’t sure I could import already demultiplexed files or I may have not remembered :o

I am still not sure what to do about my missing barcodes.fastq.gz file…

Demultiplexed sequences are accepted — see the tutorial for more details.

Barcode files are not needed if reads are already demultiplexed.

All these questions and more are answered in the tutorials that @thermokarst linked to. In particular, check out fastq manifest formats.

I hope that helps!

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