Difficulty importing RAW illumina sequences to QIIME2

Hey there. I'm hoping to get some help importing data into QIIME2. I have received raw illumina sequences under the files R1.fastq.gz and R2.fastq.gz. There is an associated mapping file for each of these as well. According to the company which did the sequencing the format is as follows:

I'm having difficulty understanding how to bring this data into QIIME2. The manifest format seems to work only if it is oriented in all-forward or all-reverse directions. Is there any way that y'all know of that I can import these files?

Thanks so much for helping.

Hey there @willwcb --- we aren't affiliated with Mr. DNA, but it looks like they have a tool for demuxing called "FASTQ Processor" --- I would link to it, but for some reason the site's URL doesn't update, so I will attach a screenshot, instead:

Try running that on these data, this should give you demuxed (e.g. per-sample) fastq or fastq.gz files. Once you have those, use the manifest format to import into QIIME 2. :qiime2:

Hey there.

I have tried this, but I’m not sure using this program is really going to be acceptable for academic work, because it is opaque. I am also having difficulty with its output, and would like to be able to produce these results myself.

Do you happen to have any idea of how I might be able to do this conversion myself? If you can point me toward any resources that might help I would greatly appreciate it.

Thank you.

See this topic — looks like others have posted a couple non-QIIME 2 alternatives there for combing mixed-orientation reads. You can re-orient, then import to QIIME 2.

Good luck!

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