MiSeq output and analysis folder quick reference guide
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Overview of data processing for MiSeq Control Software (MCS) v3 and lower
MCS images each cycle, and writes each TIFF (Tag Image File Format) image to D:\Illumina\MiSeqTemp\ [run folder]\Images\L001
Real Time Analysis (RTA) processes the TIFFs from Images folder into CIFs (Crystallographic Information Files) in D:\Illumina\MiSeqTemp\ [run folder]\Processed
RTA processes CIFs into Basecall .bcl files in the output folder.
RTA copies .bcls from output back to the analysis folder.
Secondary Analysis Software converts .bcls in D:\Illumina\MiSeqAnalysis\ [run folder]\Data\Intensities\Basecalls into FASTQ files.
In MCS v2.6 and earlier Miseq Reporter (MSR) performs secondary analysis.
In MCS v3.1 Local Run Manager (LRM).
Secondary Analysis Software writes FASTQ files from D:\Illumina\MiSeqAnalysis\ [run folder]\Data\Intensities\Basecalls to the output folder.
Overview of data processing for MCS v4 and higher
MCS images each cycle, and writes each TIFF image to D:\Illumina\RTATemp\ [run folder]\Images\L001
RTA processes the TIFFs from Images folder into CIFs in D:\Illumina\MiSeqTemp\ [run folder]\Processed
RTA processes CIFs into Basecall .bcl files in the output folder.
RTA copies .bcls from output back to the analysis folder.
Local Run Manager (LRM) converts .bcls in D:\Illumina\MiSeqAnalysis\ [run folder]\Data\Intensities\Basecalls into FASTQ files.
LRM writes FASTQ files from D:\Illumina\MiSeqAnalysis\ [run folder]\Data\Intensities\Basecalls to the output folder.
In MCS v3.1 and later, Local Run Manager Replaces MiSeq Reporter
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