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DRAGEN Single Cell RNA
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DRAGEN Single Cell RNA
  • Introduction
  • Get Started
    • Prerequisites
  • Run Set Up
    • Sample Sheet Introduction
    • Run Planning in BaseSpace Sequence Hub
    • Sample Sheet Requirements
    • Manual Launch on BaseSpace
  • Analysis Methods
    • FASTQ Processing
    • Error Correction
    • Transcript Counting
    • PIPseq CRISPR Mode
  • Analysis Results
    • Accessing Results
    • DRAGEN Report
      • Single-Cell RNA
      • Single-Cell Clustering
      • Trimmer
      • DRAGEN FastQC
      • Mapping
    • Secondary Analysis Results
  • Tertiary Analysis
    • Illumina Connected Multiomics
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  • [Sequencing_Settings]
  • [BCLConvert_Settings]
  • [BCLConvert_Data]
  • [Cloud_DragenSingleCellRna_Settings]
  • [Cloud_DragenSingleCellRna_Data]
  • [Cloud_Settings] for Auto-launch
  • [Cloud_Data] for Auto-Launch

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  1. Run Set Up

Sample Sheet Requirements

PreviousRun Planning in BaseSpace Sequence HubNextManual Launch on BaseSpace

Last updated 3 months ago

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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

[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 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

Run Planning in BaseSpace Sequence Hub