By default, MiSeq Reporter allows up to 1 mismatch when demultiplexing an indexed MiSeq run. Can I force the software to perform exact matches while demultiplexing the run? Is there an option that can be set in the sample sheet, for example?
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Looking at the MiSeq reporter manual it does not look like there is a way to do that. Have you tried to contact illumina tech support (this may be a non-documented feature)? -
Thanks for your help, according to the Illumina tech support it is not possible. This is the answer: "MSR demultiplexes with a mismatch of 1. This is not configurable. If you'd like to demultiplex with a different mismatch, I'd advise exploring bcl2fastq1.8.4."Comment
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