Analysis Config File (Optional)

The analysis configuration file is an optional input to the DRAGEN StrataMap pipeline. It is a JSON file that specifies parameters for alignment, filtering, normalization, and tertiary analysis.

Example Analysis Config

{
  "mt_threshold": 50,
  "include_only_uniquely_aligned": false
}

Secondary Analysis Parameters

Parameter	Description	Default value
bin_sizes	Size of the grid bins used in the analysis, in microns.	10
expansion_um	The cell-border expansion distance, in microns, applied to detected nuclei.	5
mitochondrial_chr	Names used for the mitochondrial chromosome so that mtRNA percentage is calculated correctly. Only required when using a custom genome that does not match any of the default names.	"chrm,m,mt"
output_nuclei_bin_results	Determines whether nuclei-bin results are included in the output.	false
include_introns	Include intronic reads in the analysis.	false
include_only_uniquely_aligned	Include only uniquely aligned reads in the analysis, excluding multimappers.	false
mapping_parameters_for_DRAGEN	Pass any parameter that affects DRAGEN alignment. See below for details.	None

mapping_parameters_for_DRAGEN Explained

To allow for customized analysis parameters in DRAGEN, the pipeline accepts any valid DRAGEN alignment parameter through this argument. For a complete list of options, see the DRAGEN product guide: here.

For example, to increase the threshold for an acceptable alignment, you could pass:

{
  "mapping_parameters_for_DRAGEN": "--Aligner.aln-min-score=50"
}

To pass more than one argument, separate them with a space in a single JSON entry:

{
  "mapping_parameters_for_DRAGEN": "--Aligner.aln-min-score=50 --Aligner.mismatch-pen=5"
}

Tertiary Analysis Parameters

Parameter	Description	Default value
mt_threshold	Filters out cell or grid bins with a higher percentage of mitochondrial transcripts than the specified threshold.	40
umi_count_threshold or umi_percentile_threshold	Filters out cell or grid bins with fewer unique molecules than the specified count threshold, or below the specified percentile threshold. Note: These parameters are mutually exclusive. Specify only one.	100 or 5th percentile If neither is specified, whichever value is higher is used.
normalize_target_sum	Sets the total transcript count for each cell or grid bin so that every cell has the same total count after normalization.	Median count prior to normalization
top_n_genes	Filters out low-variability genes, keeping only the specified number of highest-variability genes.	3000
umap_min_dist	The minimum distance between points in the Uniform Manifold Approximation and Projection (UMAP) embedding. Smaller values preserve local structure better, while larger values emphasize global relationships.	0.5
leiden_resolution	Controls the resolution parameter in Leiden clustering. Higher values typically produce more, smaller clusters, while lower values produce fewer, larger clusters.	1

Other Parameters

These parameters should not be used unless explicitly directed by support.

Parameter	Description	Default value
override_cycles	Override the default sequencing cycles for specific protocols.	"I30;N22U7Y71;N8"
override_reads	Override the default read lengths for specific protocols.	"I30;Y100;I8"