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When is the demultiplexing summary generated for analyzed MiSeq runs?
A demultiplexing summary file called DemultiplexSummaryF1L1.txt, is generated once analysis is completed through Local Run Manager or MiSeq Reporter, depending on the version of MiSeq Control Software installed. This file can be located in the following folder on the instrument:
MiSeq Reporter *D:\Illumina\MiSeqAnalysis[Run_Folder]\Data\Intensities\BaseCalls\Alignment*
Local Run Manager (LRM) v2.0 and v3.0 D:\Illumina\MiSeqAnalysis[run folder]\Alignment_#[date and time folder]