# 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](https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-output-and-analysis-folders-qrc-15034791-c.pdf)\
In MCS v3.1 and later, Local Run Manager Replaces MiSeq Reporter

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-fe5a34a497bdfd61899157aa221b76a9c89c2f5a%2Fimage1.jpg?alt=media\&token=850025f4-c7de-43e2-a133-85fc04e4b323)

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-6986550b49d10c6c7b605b279514084128ad7a2f%2Fimage2.jpg?alt=media\&token=d185d511-70b2-4010-a4d8-af93047a02ad)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #5817), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005817%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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