Multiplexing fastq files paired end without barcode file

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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