File paths for the NextSeq 500/550
The run folders on the NextSeq 500/550 include run data, along with many files that are helpful for reviewing run performance and troubleshooting, if necessary.
NextSeq Control Software (NCS) 2.2.x and 4.0.x Run Folder: The file path of each run folder is:
D:\Illumina\NextSeq Control Software Temp[Run_Folder]
Key files in this location include:
Runinfo.xml
Runparameters.xml
InterOp folder
Thumbnail Images
SampleSheet.csv
Cycle Logs:
(D:\Illumina\ NextSeq Control Software Temp [Run_Folder]\Logs)
Diagnostic.00.log:
(D:\Illumina\ NextSeq Control Software Temp [Run_Folder]\Logs)
Focus Images:
(D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Images\Focus\L00X\C1.1)
RTA Logs:
(D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\RTALogs)
RTA Config:
(D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Data\Intensities\RTAConfiguration.xml)
FirmwareVersions.txt:
(D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Config)
DemultiplexSummaryF1L1.txt
(Generated after FASTQ generation completes): [run folder]\Alignment_#[date and time folder]
BCL Files (raw data output from sequencing) are saved in 2 locations:
D:\Illumina\NextSeq Control Software Temp[Run Folder]\Data\Intensities\Basecalls
[Output Folder][Run Folder]\Data\Intensities\Basecalls
Additional helpful file paths:
NCS Logs in Windows 7: (C:\Illumina\NextSeq Control Software\Logs)
NCS Logs in Windows 10: (D:\Illumina\NextSeq Control Software\Logs)
Maintenance Logs: (D:\Illumina Maintenance Logs)
Preventative Maintenance (PM): D:\Illumina\PreventativeMaintenance
NextSeq Control Software Config: (C:\ProgramData\Illumina\NextSeq Control Software\InstrumentShell.NextSeqControlSoftware.Options.cfg)
BaseSpace Broker Logs: D:\Illumina\BaseSpace broker (NCS 2.2.x only)
Restart Universal Copy Service (UCS): (C:\ProgramFiles\Illumina\UniversalCopyService\ucs.exe) (NCS 4.0.x only)
System Check Results (all): D:\Illumina\SystemCheckResults
Beadarray folder: (The NextSeq 550 can be used to scan select beadarrays.)
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Config folder
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Focus folder
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Logs folder
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\GTC files
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\IDAT files
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Image files
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode][Barcode]_sample_metrics.csv
[Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode][Barcode]_section_metrics.csv
[Date]_[Instrument Name]_[Scan#]_[Barcode]\ScanrParameters.xml
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