Hi, I am new to Qiime2. I do not know how to create a barcode.fastq.gz file or a metadata file. I just got some paired-end sequences that my advisor gave me after we ran the Miseq together. Just the two reads per well no other files. I emailed my advisor about the barcode.fastq.gz file and told me "they are the indexes". I do have an excel sheet that I uploaded to the Miseq, I used two indexes per well (i.e N701-C TAAGGCGA S513-C TCGACTAG). I hope I am providing the right information for my question. Any help would be appreciated.
I think your best bet is to follow the following tutorial:
From what you describe, you should have dual-barcode index, so you can import the fastq files you have and then demultiplex them using cutadapt, the command are summarised here:
(but is referring to an old version of QIIME2 so it may need some tweaking ...)
Hope it helps
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