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Set up Secondary Analysis

Configure the settings for the analysis type selected for your run.

ClosedIllumina DRAGEN BCL Convert

Use the following steps to configure Illumina DRAGEN BCL Convert analysis.

1. Enter the following optional settings.

Setting

Description

AdapterRead1

Adapter sequence for read 1. If using an Illumina library prep kit, leave the AdapterRead1 field empty.

AdapterRead2

Adapter sequence for read 2. If using an Illumina library prep kit, leave the AdapterRead2 field empty.

BarcodeMismatchesIndex1

The number of allowed mismatches between the first index read and index sequence. Allowed values are 0,1, or 2. The default value is 1.

BarcodeMismatchIndex2

The number of allowed mismatches between the second index read and index sequence. Allowed values are 0,1, or 2. The default value is 1.

OverrideCycles

String used to specify UMI cycles and mask out cycles of a read. The following values are allowed:

• Y—Specifies a sequencing read.
• I—Specifies an indexing read.
• U—Specifies a UMI length to be trimmed from the read.

Each element is separated by semicolons. The following is an example of OverrideCycles input.

N1Y150;I8;I7N1;Y141U10

2. Complete the run configuration.
• To send the run configuration to your BaseSpace Sequence Hub account, select Submit Run. Runs submitted to BaseSpace Sequence Hub appear in the planned runs list and are available for systems using Cloud mode or Hybrid mode.
• To save the run configuration as a sample sheet in v2 file format, select Export Sample Sheet from the Submit Run drop-down list. The sample sheet is required to initiate runs on systems using Local mode.
ClosedIllumina DRAGEN Enrichment

Use the following steps to configure Illumina DRAGEN Enrichment analysis.

1. Select a reference genome.

If using Nextera Flex for Enrichment with the Illumina Exome Panel, only hg19 and hs37d5 reference genomes are compatible with the DRAGEN Enrichment pipeline.

2. Select a *.bed file containing the regions you would like to target or upload a new custom file.
3. Select a map/align output format.
4. Complete the run configuration.
• To send the run configuration to your BaseSpace Sequence Hub account, select Submit Run. Runs submitted to BaseSpace Sequence Hub appear in the planned runs list and are available for systems using Cloud mode or Hybrid mode.
• To save the run configuration as a sample sheet in v2 file format, select Export Sample Sheet from the Submit Run drop-down list. The sample sheet is required to initiate runs on systems using Local mode.
ClosedIllumina DRAGEN Germline

Use the following steps to configure Illumina DRAGEN analysis.

1. Select your reference genome.
2. Select a map/align output format.
3. Complete the run configuration.
• To send the run configuration to your BaseSpace Sequence Hub account, select Submit Run. Runs submitted to BaseSpace Sequence Hub appear in the planned runs list and are available for systems using Cloud mode or Hybrid mode.
• To save the run configuration as a sample sheet in v2 file format, select Export Sample Sheet from the Submit Run drop-down list. The sample sheet is required to initiate runs on systems using Local mode.
ClosedIllumina DRAGEN RNA

Use the following steps to configure Illumina DRAGEN RNA analysis.

1. Select your reference genome.
2. Select your map/align output format.
3. Select a Gene Transfer Format (GTF) file.
4. Complete the run configuration.
• To send the run configuration to your BaseSpace Sequence Hub account, select Submit Run. Runs submitted to BaseSpace Sequence Hub appear in the planned runs list and are available for systems using Cloud mode or Hybrid mode.
• To save the run configuration as a sample sheet in v2 file format, select Export Sample Sheet from the Submit Run drop-down list. The sample sheet is required to initiate runs on systems using Local mode.