Can the MiSeq System generate FASTQ files?

Can the MiSeq System generate FASTQ files? Yes. FASTQ files are generated during secondary analysis by MiSeq Reporter (MiSeq Software 2.6.2 or below) or Local Run Manager (MiSeq Software 3.1 or above) for most analysis workflows. To generate only FASTQ files, specify the GenerateFASTQ workflow in the sample sheet or during run planning in Local Run Manager to generate FASTQ files with no subsequent on-board analysis steps.

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