How to make sure FASTQ generation occurs in MiSeq Reporter when using BaseSpace for analysis
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On MiSeq control software v2.6 or lower, users have the option to replicate analysis locally when uploading to BaseSpace Sequencing Hub for analysis. To enable, open the MiSeq Control Software, select Run Options.
Select option: When using BaseSpace, replicate analysis locally on MiSeq
Select Save and Return
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