Set Up Secondary Analysis

Use the following steps to configure DRAGEN BCL Convert analysis.

1.

[Optional] Enter a description for the configuration.

2.

Select your library prep and index adapter kits.

3.

Enter the following optional settings.

4.

Use one of the following options to enter your sample information for the samples used in DRAGEN BCL Convert analysis.

•

Enter sample information in a *.csv file by selecting Download Template. To import the edited sample template, select Import Samples, and then select the CSV file.

•

Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

•

Manually enter sample IDs and corresponding lane, well positions or indexes, barcode mismatches, and project. If Not Specified is selected for the library prep kit, enter Index 1 (i7) and Index 2 (i5) sequences in the forward orientation.

5.

Select Next, and then review the run details.

6.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

7.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.

Use the following steps to configure DRAGEN Enrichment analysis.

1.

[Optional] Enter a description for the configuration.

2.

Select your library prep and index adapter kits.

3.

Select a reference genome.

If possible, use a reference genome with alt mask. For instructions on importing custom reference genomes, refer to Import Reference Genomes.

4.

Select the germline or somatic variant type.

5.

Select a variant calling workflow. If you select None, only alignment is performed. If you select All, the following variant calling workflows are performed.

•

Small variant caller

•

Structural variant caller

•

Copy number variant (CNV) caller (if panel of normals file is provided)

6.

Select a BED file containing the regions you would like to target or upload a new custom file. A BED file is only required if performing small or all variant calling.

Make sure that the reference genome for the BED file matches the reference genome selected. For instructions on importing reference files, refer to Import Reference Files.

7.

[Optional] If using the somatic variant type, select a noise baseline file.

For instructions on importing noise baseline files, refer to Import Reference Files.

8.

[Optional] If using the CNV caller, select a panel of normal files.

For instructions on importing panel of normal files, refer to Import Reference Files.

9.

Enter the following optional settings.

10.

Use one of the following options to enter your sample information for the samples used in DRAGEN Enrichment analysis.

•

Enter sample information in a *.csv file by selecting Download Template. To import the edited sample template, select Import Samples, and then select the CSV file.

•

Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

•

Manually enter sample IDs and corresponding lane, well positions or indexes, barcode mismatches, and project. If Not Specified is selected for the library prep kit, enter Index 1 (i7) and Index 2 (i5) sequences in the forward orientation.

11.

Select a map/align output format.

The Analysis Settings section uses the settings in the first Enrichment configuration created for the sequencing run. To modify the settings, edit the first Enrichment configuration.

12.

Select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.

13.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

14.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.

Use the following steps to configure DRAGEN RNA analysis.

1.

[Optional] Enter a description for the configuration.

2.

Select your library prep and index adapter kits.

3.

Select a reference genome.

If possible, use a reference genome with alt mask. For instructions on importing custom reference genomes, refer to Import Reference Genomes.

4.

[Optional] Select an RNA annotation file.

For information on adding a new RNA annotation file, refer to Import Reference Files.

5.

[Optional] Select Yes to enable down-sampling.

6.

If down-sampling, select the number of reads to down-sample.

7.

Enter the following optional settings.

8.

Use one of the following options to enter your sample information for the samples used in DRAGEN RNA analysis.

•

Enter sample information in a *.csv file by selecting Download Template. To import the edited sample template, select Import Samples, and then select the CSV file.

•

Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

•

Manually enter sample IDs and corresponding lane, well positions or indexes, barcode mismatches, and project. If Not Specified is selected for the library prep kit, enter Index 1 (i7) and Index 2 (i5) sequences in the forward orientation.

9.

Select a map/align output format.

The Analysis Settings section uses the settings in the first RNA configuration created for the sequencing run. To modify the settings, edit the first RNA configuration.

10.

Select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.

11.

Select the pipeline mode to perform. The pipeline mode determines the output files generated. The full pipeline output includes gene fusion detection and gene expression quantification.

12.

If performing the full pipeline mode, select whether to enable differential expression.

13.

If you enabled differential expression, select a control or comparison value for each sample. Manually select the information or download the import samples template, modify the analysis comparison group, and then import the edited template. Use the following guidelines when selecting analysis comparison values:

•

If the sample does not contain a control or comparison value, select NA as the value or leave the value blank.

•

In each analysis group, any sample marked as control is compared with all samples marked as comparison.

•

Each analysis group must have 2–15 control samples and 2–15 comparison samples.

•

Analysis groups should not be reused between RNA analysis configurations with different reference genomes or RNA gene annotation files.

14.

Select Next, and then review the run details.

15.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

16.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.

Use the following steps to configure DRAGEN Germline analysis.

1.

[Optional] Enter a description for the configuration.

2.

Select your library prep and index adapter kits.

3.

Select a reference genome.

If possible, use a reference genome with alt mask. For instructions on importing custom reference genomes, refer to Import Reference Genomes.

4.

Select a variant calling workflow. If you select None, only alignment is performed. If you select All, the following variant calling workflows are performed.

•

Small variant caller

•

Structural variant caller

•

Copy number variant (CNV) caller

•

Repeat expansion detection

•

CYP2D6 caller

•

Regions of homozygosity (ROH) caller

5.

[Optional] Select a QC coverage BED file. Available on DRAGEN 4.1.23 and later.

For instructions on importing reference files, refer to Import Reference Files.

6.

[Optional] Select a QC cross contamination VCF file. Available on DRAGEN 4.1.23 and later.

For instructions on importing reference files, refer to Import Reference Files.

7.

Enter the following optional settings.

8.

Use one of the following options to enter your sample information for the samples used in DRAGEN Germline analysis.

•

Enter sample information in a *.csv file by selecting Download Template. To import the edited sample template, select Import Samples, and then select the CSV file.

•

Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

•

Manually enter sample IDs and corresponding lane, well positions or indexes, barcode mismatches, and project. If Not Specified is selected for the library prep kit, enter Index 1 (i7) and Index 2 (i5) sequences in the forward orientation.

9.

Select a map/align output format.

The Analysis Settings section uses the settings in the first Germline configuration created for the sequencing run. To modify the settings, edit the first Germline configuration.

10.

Select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.

11.

Select Next, and then review the run details.

12.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

13.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.

Use the following steps to configure DRAGEN Somatic analysis.

1.

[Optional] Enter a description for the configuration.

2.

Select your library prep and index adapter kits.

3.

Select a reference genome.

If possible, use a reference genome with alt mask. For instructions on importing custom reference genomes, refer to Import Reference Genomes.

4.

Select a variant calling workflow. If you select None, only alignment is performed. If you select All, the following variant calling workflows are performed.

•

Small variant caller

•

Structural variant caller

•

Copy number variant (CNV) caller

5.

[Optional] If using the somatic variant type, select a somatic noise baseline file.

For instructions on importing noise baseline files, refer to Import Reference Files.

6.

[Optional] To generate an output that annotates potential germline variant calls, select a germline tagging file.

For instructions on importing reference files, refer to Import Reference Files.

7.

[Optional] For population allele frequencies using CNV analysis, select an AuxCnvPopBAlleleVcfFile.

For instructions on importing reference files, refer to Import Reference Files.

8.

[Optional] If using the structural variant type, select a structural variant noise baseline file.

For instructions on importing noise baseline files, refer to Import Reference Files.

9.

Enter the following optional settings.

10.

Use one of the following options to enter your sample information for the samples used in DRAGEN Somatic analysis.

•

Enter sample information in a *.csv file by selecting Download Template. To import the edited sample template, select Import Samples, and then select the CSV file.

•

Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

•

Manually enter sample IDs and corresponding lane, well positions or indexes, barcode mismatches, and project. If Not Specified is selected for the library prep kit, enter Index 1 (i7) and Index 2 (i5) sequences in the forward orientation.

11.

Select a map/align output format.

The Analysis Settings section uses the settings in the first Somatic configuration created for the sequencing run. To modify the settings, edit the first Somatic configuration.

12.

Select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.

13.

Select Next, and then review the run details.

14.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

15.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.

Use the following steps to configure DRAGEN Methylation analysis.

1.

[Optional] Enter a description for the configuration.

2.

Select your library prep and index adapter kits.

3.

Select a reference genome.

If possible, use a reference genome with alt mask. For instructions on importing custom reference genomes, refer to Import Reference Genomes.

4.

Select the methylation protocol.

5.

Enter the following optional settings.

6.

Use one of the following options to enter your sample information for the samples used in DRAGEN Methylation analysis.

•

Enter sample information in a *.csv file by selecting Download Template. To import the edited sample template, select Import Samples, and then select the CSV file.

•

Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select +. Sample IDs can contain up to 100 alphanumeric characters, hyphens, and underscores.

•

Manually enter sample IDs and corresponding lane, well positions or indexes, barcode mismatches, and project. If Not Specified is selected for the library prep kit, enter Index 1 (i7) and Index 2 (i5) sequences in the forward orientation.

7.

Select a map/align output format.

The Analysis Settings section uses the settings in the first Methylation configuration created for the sequencing run. To modify the settings, edit the first Methylation configuration.

8.

Select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.

9.

Select whether Taps is used.

10.

Select Next, and then review the run details.

11.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

12.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.