Sample Sheet Fields
A sample sheet is required to kick off secondary analysis. It can be made either using the BSSH Run Planner Tool (recommended), Excel Sample Sheet Generator, or manually. The following table describes the sample sheet fields and its values depending on the environment used to execute the DRAGEN Protein Quantification application. The pipeline can be executed via cloud using either Illumina Connected Analytics or Base Space Sequence Hub, or executed locally using a phase 4 DRAGEN Server.
Sample Sheet Fields
This is a non comprehensive list of fields.
Header
FileFormatVersion
Must be "2"
Header
InstrumentPlatform
Must be "NovaSeqXSeries" or "NovaSeq"
Header
RunName
User-provided value
Header
RunDescription
User-provided value (optional)
Reads
Read1Cycle
15
Reads
Index1Cycle
10
Reads
Index2Cycle
10
Sequencing_Settings
LibraryPrepKits
Must be "IlluminaProteinPrep9k"
BCLConvert_Data
Sample_ID
Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)
BCLConvert_Data
Index
i7 index sequence, including A, C, T or G letters, 10 nucleotides long
BCLConvert_Data
Index2
i5 index sequence, including A, C, T or G letters, 10 nucleotides long
BCLConvert_Data
Lane
Lane value (shall be a number between 1 and 8 inclusive) (optional if instrument is NovaSeq 6k, required if instrument is NovaSeq X)
Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)
SoftwareVersion
Three-digit version of SW used in secondary analysis. For example, "2.0.0"
Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)
StartsFromFastq
Must be "false"
Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)
output_file_prefix
User-provided prefix
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
Sample_ID
Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
PlateBarcode
For each plate, associated plate barcode
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
MatrixTubeBarcode
For each plate, associated matrix tube barcode
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
BatchID
For each plate, user-provided batchID
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
InputType
For each sample, associated input type. Examples: Plasma_Calibrator, Plasma_QC, Plasma, Serum_Calibrator, Serum_ QC, Serum, Blank
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
ControlID
ID of the calibrator, QC, and blank lot (applied to controls only).
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
ProbePlate
For each plate, probe plate lot number, from library prep
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
SOMAmerBeadPlate
For each plate, SOMAmer Bead Plate lot number, from library prep
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)
WellPosition
For each sample, well position (A1-H12)
Cloud_Settings
GeneratedVersion
Software version of the BSSH Run Planner tool that generated the sample sheet
Cloud_Settings
Cloud_Proteomics_Pipeline (Cloud Only)
ICA Path to the proteomics pipeline.
For example: urn:ilmn:ica:pipeline:6475f989-f9fc-4874-9ff6-10ac23d11681#DRAGEN_Protein_Quantification_2-0-0
Cloud_Data
Sample_ID
Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)
Cloud_Data
ProjectName
(optional) user-provided plate-specific project
Cloud_Data
LibraryName
For each sample, must be <Sample_ID>_<index>_<index2>
Cloud_Data
LibraryPrepKitName
Must be "IlluminaProteinPrep9k"
Cloud_Data
IndexAdapterKitName
Must be "IlluminaDNARNAUDISetABCDTagmentation_Proteomics"
Samplesheet Examples
Examples of local and cloud sample sheets for NovaSeq 6000 and NovaSeq X are attached to this page.
Local
Cloud
For additional information, refer to the ICS Samplesheet documentation.
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