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File Paths on the iSeq 100

**iSeq100 File Paths:
Temp Run Folder**: D:\Illumina\iSeq Runs[RunFolder]
  • InterOp
  • 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
For any feedback or questions regarding this article (Illumina Knowledge Article #2287), contact Illumina Technical Support [email protected].
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