Problems with fastq files paired end without barcode file

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Hi @RAVargasC,

I am guessing that you mean you don't have a separate barcodes.fastq file, but do have the BarcodeSequence used inside your mapping file-right? If so, that is usually how I receive my data and barcodes are located at the beginning of my R1 and R2 fastq files. I use 12 bp golay barcodes when sequencing and these can easily be extracted and then you can follow the qiime 2 tutorial.

  1. extract_barcodes.py using qiime1
  2. Import data using qiime2 .
    3.Follow Moving Pictures Tutorial to demultiplex, denoise, ect..
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Where to Start from with R1 and R2 files