Sample Sheet Requirements

The DRAGEN Single Cell RNA software has optional and required fields in addition to general sample sheet requirements. Below is a description of the fields in each section.

The preferred method for creating sample sheets is to use Run Planning in BaseSpace Sequence Hub

[Sequencing_Settings]

Parameter	Required?	Details
LibraryPrepKits	Required	Accepted values are: IlluminaSingleCell3RNAPrep

[BCLConvert_Settings]

Parameter	Required?	Details
SoftwareVersion	Required	The DRAGEN component software version. DRAGEN Single Cell RNA software requires 4.4.0.
NoLaneSplitting	Required	TRUE for DRAGEN Single Cell RNA software
TrimUMI	Required	0 for DRAGEN Single Cell RNA software
OverrideCycles	Required	U45;I10;I10;Y72 for DRAGEN Single Cell RNA software. May be different if running multiple applications in a single run.
FastqCompressionFormat	Required	gzip

[BCLConvert_Data]

Parameter	Required?	Details
Sample_ID	Required	Must match a Sample_ID listed in the [Cloud_DragenSingleCellRna_Data] and [Cloud_Data] section.
Index	Required	Index 1 sequence
Index2	Required	Index 2 sequence
Lane	Only for NovaSeq 6000/6000 Dx workflow	Indicates which lane corresponds to a given sample. Enter a single numeric value per row. Cannot be empty, i.e. the analysis fails if the Lane column is present without a value in each row.

[Cloud_DragenSingleCellRna_Settings]

Parameter	Required?	Details
SoftwareVersion	Required	The DRAGEN component software version. DRAGEN Single Cell RNA software requires 4.4.0.
EnablePipseqMode	Required	TRUE for Illumina Single Cell 3’ RNA kit. Maps to --scrna-enable-pipseq-mode in command line arguments.
ReferenceGenomeDir	Required	Location of reference genome TAR containing a DRAGEN hash table and optionally a GTF.
BarcodeRead	Required	Read1 for Illumina Single Cell 3’ RNA kit
RnaLibraryType	Required	SF for Illumina Single Cell 3’ RNA kit (stranded forward). Maps to --rna-library-type in command line arguments.
BarcodePosition	Required	0_7+11_16+20_25+31_38 for Illumina Single Cell 3’ RNA kit. Maps to --scrna-barcode-position in command line arguments.
UmiPosition	Required	39_41 for Illumina Single Cell 3’ RNA kit. Maps to --scrna-umi-position in command line arguments.

[Cloud_DragenSingleCellRna_Data]

Parameter	Required?	Details
Sample_ID	Required	Must match a Sample_ID listed in the [BCLConvert_Data] and [Cloud_Data] section.

[Cloud_Settings] for Auto-launch

Parameter	Required?	Details
GeneratedVersion	Not Required	The cloud GSS version used to create the sample sheet. Optional if manually updating a sample sheet. (ex: 1.17.0.202411192008).
Cloud_Workflow	Not Required	ica_workflow_1
BCLConvert_Pipeline	Required	The value is a universal record number (URN). The valid value is: urn:ilmn:ica:pipeline:730df76f-715a-45bf-9500-e6e0ce1ab224#BclConvert_v4_3_13
Cloud_DragenSingleCellRna_Pipeline	Required	The value is a URN in the following format: urn:ilmn:ica:pipeline:b3c5ab5f-2853-4873-93c4-61a807f844a7#DRAGEN_Single_Cell_RNA_4-4-2_-_Sequencer_Integration_Only

[Cloud_Data] for Auto-Launch

Parameter	Required?	Details
Sample_ID	Required	Must match a Sample_ID listed in the [BCLConvert_Data] and [Cloud_DragenSingleCellRna_Data] section.
ProjectName	Not Required	The BaseSpace Sequence Hub project name
LibraryName	Not Required	Combination of sample ID and index values in the following format: sampleID_Index_Index2.
LibraryPrepKit	Required	The Library Prep Kit used
IndexAdapterKitName	Required	The Index Adapter Kit used