# File Paths on the iSeq 100

**iSeq 100 File Paths:**

**Temp Run Folder:** D:\Illumina\iSeq Runs\[RunFolder]

* InterOp
* Data
  * \Intensities\Basecalls\L001 (to locate BCL files)
* RunParameters.xml
* RunInfo.xml
* RunCompletionStatus.xml
* Logs
* Cycles
* RTALogs
* Thumbnail\_Images
  * \L001\Cx.1 (where "x" corresponds to cycle number)
* SampleSheet.csv

**Default Output Run Folder**: D:\SequencingRuns\[RunFolder]

* InterOp
* RunParameters.xml
* RunInfo.xml
* RunCompletionStatus.xml
* Logs
* Cycles
* RTALogs
* Thumbnail\_Images
  * \L001\Cx.1 (where "x" corresponds to cycle number)
  * \NormalizedFC for a zoomed out picture of flow cell (will be useful in certain troubleshooting instances)
* SampleSheet.csv

**Secondary Analysis Files:** Present when Local Run Manager performed secondary analysis.

* LRM Default location: D:\Illumina\SequencingRuns\[Runfolder]\Alignment\_1 where "alignment #" is the number of the analysis/requeue, such as "1" for the initial analysis
  * Demultiplex\_Stats.csv
  * Top\_Unknown\_Barcodes.csv
  * IndexMetricsOut.bin
  * SampleSheet.csv

**Pre-Run Check Logs**: D:\Illumina\iSeq Pre Run Checks

* Images
* Logs
* Reports

**System Check Results**: D:\Illumina\iSeq System Checks

**Control Software Logs**: C:\Program Files\Illumina\iSeqSbsControlSoftwareServer\Logs

**Universal Copy Service (UCS) Logs**: C:\ProgramData\*\Illumina\UniversalCopyService\Logs\
\*The ProgramData folder may be hidden. To un-hide files, click on the View tab in the File Explorer window and ensure the box for “Hidden items” is checked.

**Security Settings:** C:\Illumina\Security

* Enable.reg
* Disable.reg

**CloudAPIKey**

* C:\ProgramData\Illumina
  * cloudAPI.xml

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