Sample Sheet Creation in BaseSpace Run Planning tool
How to Create TSO 500 Sample Sheets in BaseSpace Run Planning tool
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.
Step 1: Run Settings
| 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:
|
Secondary Analysis | Required |
|
Read 1 | Required on Instrument Platform NovaSeq X Series |
|
Index 1 | Required on Instrument Platform NovaSeq X Series |
|
Index 2 | Required on Instrument Platform NovaSeq X Series |
|
Read 2 | Required on Instrument Platform NovaSeq X Series |
|
Sample Container ID | Optional |
|
Step 2: Configuration
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.
| Parameter Name | Required | Description |
|---|---|---|
Application* | Required |
|
Description | Optional | Optional text field |
Library Prep Kit | Required |
|
Index Adapter Kit | Required | TSO 500:
TSO 500 HT:
|
Step 3: Sample Settings
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.
| Parameter Name | Required | Description |
|---|---|---|
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. |
Step 4: Run Review
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.
Planned Runs Screen (NovaSeq X Series only)
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.
Guided Examples
Please review these guided examples of analysis workflows that include a step of setting up a run in BaseSpace Run Planning tool:
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