Configure the settings for the analysis type selected for your run.
Each element is separated by semicolons. The following is an example of OverrideCycles input: N1Y150;I8;I7N1;Y141U10
Cloud or Hybrid mode — Select Upload Custom File (BaseSpace). The custom BED file is only available in the Workgroup it was uploaded to.
3- Select either the germline or somatic variant caller
4- [Optional] If using the somatic variant caller, select a noise baseline file.
If using the DRAGEN Enrichment workflow in somatic mode, you can use a noise baseline file to filter out sequencing or systematic noise. You can download standard custom noise files from the Illumina Support Site or create a custom noise baseline file. Refer to Custom Noise Baseline File for more information.
5- Select a map/align output format.
6- For Local mode, select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.
7- For Local mode, select one of the following FASTQ output format options:
gzip - Save the FASTQ files in gzip format
DRAGEN - Save FASTQ files in ora format
8- Review and Complete the run configuration.
To save the run configuration for further editing, select Save as Draft. Draft runs appear in BaseSpace Sequence Hub planned runs list, but will not be available on the instrument until the draft runs are saved as planned.
To send the run configuration to your BaseSpace Sequence Hub account, select Save as Planned. 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. The sample sheet and secondary analysis supporting files are downloaded in a *.zip folder and are required to initiate runs on systems using Local mode. This option is only available if Local was selected for analysis location.
DRAGEN - Save FASTQ files in ora format
5- Review and Complete the run configuration.
To save the run configuration for further editing, select Save as Draft. Draft runs appear in BaseSpace Sequence Hub planned runs list, but will not be available on the instrument until the draft runs are saved as planned.
To send the run configuration to your BaseSpace Sequence Hub account, select Save as Planned. 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. The sample sheet is required to initiate runs on systems using Local mode. This option is only available if Local was selected for analysis location.
DRAGEN - Save FASTQ files in ora format
5- [Optional] Upload a Gene Transfer Format (GTF) file for RNA Annotation file
Local mode — Select Upload Custom File (Local) to upload for a single run or Upload Custom File (BaseSpace) for repeated use.
Cloud or Hybrid mode — Select Upload Custom File (BaseSpace). The GTF file is only available in the Workgroup it was uploaded to.
6- Select whether to enable differential expression.
7- If you enabled differential expression, select a control or comparison value for each sample. In each comparison group, any sample marked as control is compared with all samples marked as comparison. If the sample does not contain a control or comparison value, select na as the value.
8- Review and Complete the run configuration.
To save the run configuration for further editing, select Save as Draft. Draft runs appear in BaseSpace Sequence Hub planned runs list, but will not be available on the instrument until the draft runs are saved as planned.
To send the run configuration to your BaseSpace Sequence Hub account, select Save as Planned. 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. The sample sheet and secondary analysis supporting files are downloaded in a *.zip folder, and are required to initiate runs on systems using Local mode. This option is only available if Local was selected for analysis location.
Cloud or Hybrid mode — Select Upload Custom File (BaseSpace). The GTF file is only available in the Workgroup it was uploaded to.
3- Select your map/align output format.
4- For Local mode, select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.
5- For Local mode, select one of the following FASTQ output format options:
gzip - Save the FASTQ files in gzip format
DRAGEN - Save FASTQ files in ora format
6- Select the configuration identical to your library prep kit type. For example, if you selected Single Cell RNA Library Kit 1 as your library prep kit, select Type 1 for the Configuration Type.
7- Select the barcode read.
8- [Optional] Edit the number of bases in the barcodes and the UMI. The values are automatically filled based on the library prep kit and configuration type you selected.
9- Select the strand orientation.
10- [Optional] Select a file containing your barcode sequences or upload a new custom file.
11- If using an Advanced/Custom configuration type, enter values for the number of override cycles, the barcode position, and the UMI position.
12- Review and Complete the run configuration.
To save the run configuration for further editing, select Save as Draft. Draft runs appear in BaseSpace Sequence Hub planned runs list, but will not be available on the instrument until the draft runs are saved as planned.
To send the run configuration to your BaseSpace Sequence Hub account, select Save as Planned. 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. The sample sheet and secondary analysis supporting files are downloaded in a *.zip folder, and are required to initiate runs on systems using Local mode. This option is only available if Local was selected for analysis location.
Cloud or Hybrid mode — Select Upload Custom File (BaseSpace). The custom BED file is only available in the Workgroup it was uploaded to.
3- Select either the germline or somatic variant caller
4- Select a map/align output format.
5- For Local mode, select whether to save a copy of your FASTQ files. FASTQ files are only generated if you select to keep FASTQ files.
6- For Local mode, select one of the following FASTQ output format options:
gzip - Save the FASTQ files in gzip format
DRAGEN - Save FASTQ files in ora format
8- Review and Complete the run configuration.
To save the run configuration for further editing, select Save as Draft. Draft runs appear in BaseSpace Sequence Hub planned runs list, but will not be available on the instrument until the draft runs are saved as planned.
To send the run configuration to your BaseSpace Sequence Hub account, select Save as Planned. 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. The sample sheet and secondary analysis supporting files are downloaded in a *.zip folder and are required to initiate runs on systems using Local mode. This option is only available if Local was selected for analysis location.