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
LibraryPrepKits
Required
Accepted values are: IlluminaSingleCell3RNAPrep
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
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.
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.
Sample_ID
Required
Must match a Sample_ID listed in the [BCLConvert_Data] and [Cloud_Data] section.
GeneratedVersion
Not Required
The cloud 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
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
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