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

For any feedback or questions regarding this article (Illumina Knowledge Article #2287), contact Illumina Technical Support [e-mail].