Multiplexing fastq files paired end without barcode file

Hello community I need your help,
I’m starting to work with qiime 2 and I have two .fastq files coming from MiSeq parsing end, no barcode file and n barcode into .fastq file. What are the steps to be able to transform it to qza and follow the analysis.
Thank you very much for your help.

Hi @nganngo281097!

Are these barcodes part of the sequences? If so, see this tutorial for advice on importing and demultiplexing: Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

If they are in the fastq header line or some other place like that, you will need to convert these to a different format prior to importing to QIIME 2. This qiime1 script might be a solution. Ideally, you would extract the barcodes and place them in a new fastq file, then import your data as EMP format in QIIME 2.

I hope that helps!

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Thank you for your help. I have only .fastq R1 file forward and fastq R2 file in reverse direction with the same sequence as above. And when I create the metadata file, there is no barcode in it. How can I analyze my data with qiime 2?

So you have only one sample? If that is the case, you can import using in the paired-end manifest format and proceed as if your data are already demultiplexed.

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