It sounds like you might have multiplexed-paired end reads with the barcodes still in the reads, which means there is no need to create a barcodes.fastq.gz. However, without more information, we can't be sure. If the barcodes are in fact in your reads, you can use this tutorial as a guide:
I recently answered a question that spells out how the mapping between barcodes and sequences work here:
Although the post is about single end sequences, the logic stands.