DAM Manual Launch

How to Launch a Manual Analysis

After DRAGEN StrataMap has been installed on the DRAGEN Server, the user can execute the run script to launch analyses. The run script requires the same inputs as the Core workflow, which can be viewed by using the --help argument. The primary difference between local and cloud execution is that the user must request a presigned URL and then download the map file to the DRAGEN Server in order to provide it to the app.

Inputs

Input arguments, folders, and files have the same requirements as listed in Analysis Inputs unless otherwise specified.

For more information about the inputs, see the Analysis Inputs page.

The following are a list of standard inputs files and folders.

BCL Folder	Sequencing run output directory	Yes
Sample Sheet	CSV file defining samples and settings	Yes
Map File	Map file (.encrypted.json)	Yes
Image Folder	OME-TIFF microscopy images	No*
Analysis Config	JSON file with analysis parameters	No
Genome	mm39 or hg38 to select one of the prepackaged genomes	No
Custom Genome (Optional)**	Path to custom genome folder	No

*Required unless running in imageless mode

**Refer to the Genomes section for instructions on creating a custom genome.

Running an Analysis

Basic Analysis with Images

The most common workflow includes microscopy images for spatial localization. The following are the minimal set of arguments to include for analysis. For additional information, call ./run_DRAGEN_StrataMap.sh --help

Optional and Advanced arguments are listed in the Advanced Options section.

Default Required Parameters

Argument	Description	Example
--input-folder	Path to BCL sequencing folder	/data/runs/230101_Run1
--samplesheet	Path to sample sheet CSV	/data/samplesheet.csv
--genome	Reference genome (mm39 or hg38)	mm39
--map-file	Path to map file	/data/map.encrypted.json
--image-folder	Path to OME-TIFF images	/data/images

Example

./run_DRAGEN_StrataMap.sh \
    --input-folder /path/to/bcl/folder \
    --samplesheet /path/to/samplesheet.csv \
    --genome mm39 \
    --map-file /path/to/map.encrypted.json \
    --image-folder /path/to/images \
    --output-dir my_analysis_results \
    --run-name "My_Experiment"

Imageless Analysis

For workflows without microscopy images, the application uses the SampleLocator feature to automatically detect sample regions. To run an imageless analysis, configure the run script with the following modifications:

• Add --run-has-images false to the run_DRAGEN_StrataMap.sh command.
• Do not include the image folder.

Example

./run_DRAGEN_StrataMap.sh \
    --input-folder /path/to/bcl/folder \
    --samplesheet /path/to/samplesheet.csv \
    --genome mm39 \
    --map-file /path/to/map.encrypted.json \
    --run-has-images false \
    --output-dir my_imageless_results \
    --run-name "My_Imageless_Experiment"

How Imageless Mode Works

SampleLocator analyzes sequencing data against the map file to automatically identify and segment tissue regions without requiring microscopy images.

Advanced Options

The following are additional input arguments available

--grid-bin-size	Grid bin size(s) in µm (colon-delimited)	10
--cell-boundary-expansion	Cell boundary expansion distance in µm	5
--include-introns	Include intronic reads in analysis	false
--output-bam	Output BAM alignment file	false
--output-nuclei-bin-results	Output nuclei-binned results	false
--analysis-config	Path to analysis configuration JSON	None
--run-has-images	Whether images are included	true
--output-dir	Output directory name	workspace
--ext-segmentation-folder	Absolute path to externalsegmentation folder	None
--run-name	Run name for run level reports	None
--include-introns	Include intronic reads	false
--resource-size	Resource Size Profile: M, L, XL	L
--help	Print help message	None
--dry-run	Create DAM payload, do not execute	None

Example: Multiple bin sizes with introns

./run_DRAGEN_StrataMap.sh \
    --input-folder /path/to/bcl/folder \
    --samplesheet /path/to/samplesheet.csv \
    --genome hg38 \
    --map-file /path/to/map.encrypted.json \
    --image-folder /path/to/images \
    --grid-bin-size "5:10:20" \
    --include-introns \
    --output-dir my_results

Outputs

Refer to the DRAGEN StrataMap Outputs section for output information:

DAM Application Specific Log Files

nextflow.log	Output directory root	Main workflow execution log
DAM_startup.log	Output directory root	Application startup log