Sample Sheet Creation in BaseSpace Run Planning tool
Last updated
Last updated
The BaseSpace Sequence Hub Run Planning tool is available, and is used to generate a valid sample sheet in v2 format for use on a TSO 500 supported sequencer for both ICA and Standalone DRAGEN Server analysis options. Filling out the form on the user interface will produce a exportable sample sheet with the required fields filled in. Refer to ICA Auto-launch Sample Sheet Requirements for descriptions of fields that appear in ICA sample sheets.
The sections below represent each step in the BaseSpace Run Planning tool.
Note that NovaSeq X Series has a different run set up configuration screen than other instrument platforms. TSO 500 does not support multi analysis, and in order to run TSO 500 on NovaSeq X Series, enter the appropriate Read 1, Read 2, Index 1 and Index 2 described in the instructions below.
BaseSpace Run Planning tool cannot generate a valid sample sheet for NovaSeq 6000Dx Analysis Application. Refer to Sample Sheet Requirements page to create a valid sample sheet.
| Parameter Name | Required | Description |
|---|---|---|
Note: On NovaSeq X Series, this page is called "Configuration 1". The right hand corner of the UI displays the Read 1, Read 2, Index 1 and Index 2 entered on the previous run settings screen.
Users can manually enter sample information, or download a template file to bulk upload sample information. Users can import the completed template or a compatible sample sheet.
Once all details are captured and pass validation, the user can review the details on the Run Review screen. From here they can choose to edit details in previous screens or export the sample sheet. Once completed, press the Cancel button to finish run planning.
Note: once leaving this screen, the run and sample sheet will not be accessible.
For NovaSeqX Plus users, the run can be saved as a draft or as a planned run (via “Save as Draft” and “Save as Planned” buttons respectively). Either selection will save the run to the Planned Runs screen on BaseSpace. There is no option to export the sample sheet on this screen.
The Planned Runs screen lists all planned or drafted runs. Users can set drafted runs to planned, export the sample sheet, and edit or delete a run on this screen.
Once the run is saved as Planned, it will appear on the NovaSeq X Series instrument where it can be selected for sequencing.
For more information on run planning, refer to the BaseSpace Sequence Hub support site page.
Please review these guided examples of analysis workflows that include a step of setting up a run in BaseSpace Run Planning tool:
| Parameter Name | Required | Description |
|---|---|---|
| Parameter Name | Required | Description |
|---|---|---|
Run Name
Required
Run Name can contain 255 alphanumeric characters, dashes, underscores, periods, and spaces; and must start with an alphanumeric, a dash or an underscore.
Run Description
Optional
Run Description can contain 255 characters except square brackets, asterisks, and commas.
Instrument Platform
Required
Choose from TSO 500 supported instruments:
NextSeq 500/550
NextSeq 1000/2000
NovaSeq 6000/6000Dx
NovaSeq X Series
Secondary Analysis
Required
BaseSpace/Illumina Connected Analytics (to generate sample sheet for cloud analysis)
Local
Read 1
Required on Instrument Platform NovaSeq X Series
Fill with value 101 for TSO 500 analysis
Index 1
Required on Instrument Platform NovaSeq X Series
Fill the value depending on the TSO 500 assay used:
TSO 500 HT: 10
TSO 500: 8
Index 2
Required on Instrument Platform NovaSeq X Series
Fill the value depending on the TSO 500 assay used:
TSO 500 HT: 10
TSO 500: 8
Read 2
Required on Instrument Platform NovaSeq X Series
Fill with value 101 for TSO 500 analysis
Sample Container ID
Optional
Unique Identifier for the container that holds the sample
Application*
Required
DRAGEN TruSight Oncology 500 Analysis Software - 2.6.0 (with HRD)
DRAGEN TruSight Oncology 500 Analysis Software - 2.6.0
Description
Optional
Optional text field
Library Prep Kit
Required
TruSight Oncology 500
TruSight Oncology 500 High Throughput
Index Adapter Kit
Required
TSO 500:
TruSight Oncology 500 (NovaSeq6000Dx with S1, S2, S4, or SP Flow Cell, NextSeq1000/2000, NovaSeqX Series)
TruSight Oncology 500 (NovaSeq6000, NextSeq)
TSO 500 HT:
TruSight Oncology 500 High Throughput (NovaSeq6000Dx with S1, S2, S4, or SP Flow Cell, NextSeq1000/2000, NovaSeqX Series)
TruSight Oncology 500 High Throughput (NovaSeq6000, NextSeq)
Read Lengths: Read 1 and Read 2
Required Not applicable on NovaSeq X Series
Auto filled with the standard values, but can be optionally overwritten.
Override Cycles
Required on NovaSeq X Series
Entered based on Run Settings read lengths & index 1 / index 2
Lane Usage
Not applicable on NovaSeq X Series or NextSeq 1000 / 2000
Checkbox allows users to apply the same lane across samples.
Lane
Required if Lane Usage is unchecked Not applicable on NextSeq 1000 / 2000
Specify lanes for each sample. The unmarked checkbox at the top of the dropdown selects all lanes.
Pair ID
Required
The identifier used to pair DNA and RNA samples in a run. The field is mandatory whether a sample is part of a pair, or not.
To note: The Sample ID field in the generated samplesheet will be auto-filled based on the Pair ID values captured. “_dna” and “_rna” (for DNA and RNA samples respectively) will be appended to the Pair ID value to create the Sample ID.
DNA Index ID
Required
Index set ID options are based on selected Index Adapter Kit
DNA Sample Feature
Required for TSO 500 HRD
Column appears when TSO 500 HRD application is selected. Enter for HRD enriched DNA Samples
RNA Index ID
Required
Index set ID options are based on selected Index Adapter Kit
Project
Optional
Optional field to describe the associated project
Starts from Fastq
Required
True or False
If auto-launching TSO 500 from BCL files, set the value to False. If auto-launching TSO 500 from FASTQ after auto-launching BCL Convert, set the value to True.
DNA Barcode Mismatches Index 1**
DNA Barcode Mismatches Index 2**
RNA Barcode Mismatches Index 1**
RNA Barcode Mismatches Index 2**
Required on NovaSeq X
Default value is set to 1.
These fields are required by NovaSeq X and represent BCL Convert settings for index diversity checks when demultiplexing. These values are not used in TSO 500 analysis.