MiSeq output and analysis folder quick reference guide
Overview of data processing for MiSeq Control Software (MCS) v3 and lower
- 1.MCS images each cycle, and writes each TIFF (Tag Image File Format) image to D:\Illumina\MiSeqTemp[run folder]\Images\L001
- 2.Real Time Analysis (RTA) processes the TIFFs from Images folder into CIFs (Crystallographic Information Files) in D:\Illumina\MiSeqTemp[run folder]\Processed
- 3.RTA processes CIFs into Basecall .bcl files in the output folder.
- 4.RTA copies .bcls from output back to the analysis folder.
- 5.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).
- 6.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
- 1.MCS images each cycle, and writes each TIFF image to D:\Illumina\RTATemp[run folder]\Images\L001
- 2.RTA processes the TIFFs from Images folder into CIFs in D:\Illumina\MiSeqTemp[run folder]\Processed
- 3.RTA processes CIFs into Basecall .bcl files in the output folder.
- 4.RTA copies .bcls from output back to the analysis folder.
- 5.Local Run Manager (LRM) converts .bcls in D:\Illumina\MiSeqAnalysis[run folder]\Data\Intensities\Basecalls into FASTQ files.
- 6.LRM writes FASTQ files from D:\Illumina\MiSeqAnalysis[run folder]\Data\Intensities\Basecalls to the output folder.
MiSeq v2.6 and earlier Output and Analysis Folder Quick Reference Guide
In MCS v3.1 and later, Local Run Manager Replaces MiSeq Reporter
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