Run

Author: SeekGene

Time: 3 min

Words: 528 words

Updated: 2026-02-27

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SeekSpace™ Tools

Run Examples

Example 1: Basic Usage

TIP

Set necessary configuration files for analysis, including sample data paths, reagent types, genome index, GTF, etc. Use the following command to run SeekSpace™ Tools:

seekspacetools run \
--fq1 /path/to/demo/demo_expression_S8_L007_R1_001.fastq.gz \
--fq2 /path/to/demo/demo_expression_S8_L007_R2_001.fastq.gz \
--spatialfq1 /path/to/demo/demo_spatial_S7_L007_R1_001.fastq.gz \
--spatialfq2 /path/to/demo/demo_spatial_S7_L007_R2_001.fastq.gz \
--hdmifq /path/to/demo/2P231224030A4.fq.gz \
--samplename demo \
--outdir /path/to/outdir \
--genomeDir /path/to/GRCh38/star \
--gtf /path/to/GRCh38/genes/genes.gtf \
--chemistry DDVS \
--core 4 \
--include-introns \
--forceCell 80000 \
--min_umi 200 \
--chip_id 2P231224030A4 \
--DAPI /path/to/demo/2P231224030A4.tif

NOTE

--HE is optional. If an HE image is provided, specify the HE image path.

Parameter Description

Parameter	Description
--fq1	Expression library R1 FASTQ data path.
--fq2	Expression library R2 FASTQ data path.
--spatialfq1	Spatial library R1 FASTQ data path.
--spatialfq2	Spatial library R2 FASTQ data path.
--hdmifq	HDMI library FASTQ data path.
--samplename	Sample name. Supports numbers, letters, and underscores only.
--outdir	Output directory. Default: ./
--genomeDir	Reference genome path built by STAR, version must match STAR used by SeekSpace™ Tools.
--gtf	GTF path for the corresponding species.
--core	Number of threads used for analysis.
--chemistry	Reagent type, each corresponds to a set of --shift, --pattern, --structure, --barcode and --sc5p combination. Options: DDVS; DDVS corresponds to Spatial Transcriptome Kit;
--skip_misB	Do not allow base mismatches in barcode. Default allows one base mismatch.
--skip_misL	Do not allow base mismatches in linker. Default allows one base mismatch.
--skip_multi	Discard Reads that can be corrected to multiple whitelist barcodes. Default corrects to the barcode with the highest proportion.
--forceCell	If this parameter is used followed by an expected number N, SeekSpace™ Tools will select the top N cells based on UMI counts from high to low. Default: 80000.
--min_umi	Minimum UMI count for cells. Cells with UMI counts lower than this value will be discarded. Default: 200.
--include-introns	When disabled, only exon Reads are used for quantification; when enabled, intron Reads are also used for quantification.
--star_path	Specify other versions of STAR path for alignment. Version must be compatible with --genomeDir version. Default --star_path is STAR in the environment.
--chip_id	Chip ID.
--DAPI	DAPI stained tissue image (TIFF).
--HE	H&E stained tissue image (TIFF).

Example 2: Support skipping Reads processing steps, adjusting images

seekspacetools realign \
--results_path /path/to/outdir \
--outdir /path/to/new_dir \
--samplename demo \
--chip_id 2P231224030A4 \
--core 4 \
--DAPI /path/to/demo/2P231224030A4.tif \
--alignment_file /path/to/demo/parameters.json \
--lenient_segmentation

NOTE

--HE is optional. If an HE image is provided, specify the HE image path.

Parameter Description

Parameter	Description
--results_path	Directory path after the first analysis of seekspacetools.
--outdir	Output directory.
--samplename	Sample name.
--chip_id	Chip ID.
--core	Number of threads used for analysis.
--DAPI	DAPI stained tissue image (TIFF).
--HE	H&E stained tissue image (TIFF).
--alignment_file	JSON file path containing image adjustment parameters.
--lenient_segmentation	Whether to enable lenient segmentation strategy.