# File Paths for the MiniSeq Control Software v2.0

The following are commonly used files and file paths for the MiniSeq.

**Temp Run Folder: This folder contains the raw sequencing data output.**

* Location: D:\Illumina\MiniSeq Sequencing Temp\<run folder>
* Folder structure: (Note: the structure of other output folders is similar.)
  * Configs
  * Data
  * Intensities\
    \- BaseCalls\
    \* L001 (Base call files, aggregated per cycle)\
    \* L001 (An aggregated \*.locs file)
  * Images\
    \- Focus\
    \* L001 — Focus images (Shows images of clustering on the flow cell prior to cycle 1 of sequencing.)
  * InstrumentAnalyticsLogs (Log files describing instrument analytics steps)
  * InterOp (Binary files used by the Sequencing Analysis Viewer software)
  * Logs (Log files describing operational steps)
  * Recipe (Run-specific recipe file named with reagent cartridge ID)
  * RTALogs (Log files describing analysis steps)
  * RTAComplete.xml (this file is a marker file that indicates RTA processing is complete. The presence of this file triggers Local Run Manager to queue analysis.)\_
  * RTAConfiguration.xml
  * RunInfo.xml
  * RunNotes.xml
  * RunParameters.xml

**MiniSeq Control Software Logs Folder**

* Location: D:\Illumina\MiniSeq Control Software

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