For a list of subcommands, run spaceranger --help.
Count gene expression and protein expression reads from a single capture area.
Usage:
spaceranger count [OPTIONS] --id <ID> --transcriptome <PATH> --create-bam <true|false> --image <IMG>|--darkimage <IMG>|--colorizedimage <IMG>|--cytaimage <IMG>
spaceranger count -h | --help | --version
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files |
--image <IMG> | Single H&E brightfield image in either TIFF or JPG format |
--darkimage <IMG> | Multi-channel, dark-background fluorescence image as either a single, multi-layer TIFF file or multiple TIFF or JPEG files |
--colorizedimage <IMG> | Color image representing pre-colored dark-background fluorescence images as either a single-layer TIFF or single JPEG file |
--cytaimage <IMG> | Brightfield image generated by the CytAssist instrument (the CytAssist image) |
--dapi-index <NUM> | Index of DAPI channel (1-indexed) of fluorescence image |
--slide <TEXT> | Visium slide serial number, for example 'V10J25-015'. Strongly recommended for Visium HD. If unknown, use --unknown-slide instead |
--area <TEXT> | Visium capture area identifier, for example 'A1' (or, e.g. 'A' for 11 mm capture area slides). Must be used along with --slide unless --unknown-slide is used |
--override-id | Overrides the slide serial number and capture area provided in the Cytassist image metadata. Use in combination with --slide and --area or with --unknown-slide |
--transcriptome <PATH> | Path of folder containing 10x-compatible reference |
--probe-set <CSV> | CSV file specifying the probe set used, if any |
--filter-probes <true/false> | Whether to filter the probe set using the "included" column of the probe set CSV. Filtering probes is recommended. See online documentation for details. (default: true) (possible values: true, false) |
--fastqs <PATH> | Path to input FASTQ data |
--project <TEXT> | Name of the project folder within a mkfastq or bcl2fastq-generated folder from which to pick FASTQs |
--sample <PREFIX> | Prefix of the filenames of FASTQs to select |
--lanes <NUMS> | Only use FASTQs from selected lanes |
--libraries <CSV> | CSV file declaring input library data sources |
--feature-ref <CSV> | Feature reference CSV file corresponding to the antibody panel used to prepare the protein expression library |
--unknown-slide <visium-1/visium-2/visium-2-large/visium-hd> | Use this option if the slide serial number and area were entered incorrectly on the CytAssist instrument and the correct values are unknown. Please see the online documentation for more information. Not compatible with --slide, --area, or --slide-file options |
--reorient-images <true/false> | Whether the pipeline should rotate and mirror the image to align the “upright hourglass” fiducial pattern in the top left corner. Only set this to false if you are certain your image is already oriented with the “upright hourglass” in the top left corner. (default: true) (possible values: true, false) |
--slidefile <GPR/VLF> | Slide design file for your slide, based on serial number and downloaded from 10x Genomics. NOTE: this is only required if your machine doesn't have internet access. You must still specify --slide and --area when using this argument |
--image-scale <FLOAT> | Microns per microscope image pixel. Only use if the microscope is well calibrated and the scale information is accurate. Scale is used to improve CytAssist to microscope image registration |
--loupe-alignment <PATH> | Alignment file produced by the Loupe Browser manual alignment step |
--create-bam <true/false> | Enable or disable BAM file generation. Setting --create-bam=false reduces the total computation time and the size of the output directory (BAM file not generated). We recommend setting --create-bam=true if unsure. See https://10xgen.com/create-bam for additional guidance (possible values: true, false) |
--nosecondary | Disable secondary analysis, e.g. clustering. Optional |
--r1-length <NUM> | Hard trim the input Read 1 to this length before analysis |
--r2-length <NUM> | Hard trim the input Read 2 to this length before analysis |
--no-libraries | Proceed with processing using a --feature-ref but no protein expression libraries specified with the --libraries flag |
--dry | Do not execute the pipeline. Generate an pipeline invocation (.mro) file and stop |
--jobmode <MODE> | Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more details on configuring the pipeline to use a compute cluster (default: local) |
--localcores <NUM> | Set max cores the pipeline may request at one time. Only applies to local jobs |
--localmem <NUM> | Set max GB the pipeline may request at one time. Only applies to local jobs |
--localvmem <NUM> | Set max virtual address space in GB for the pipeline. Only applies to local jobs |
--mempercore <NUM> | Reserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at least this much memory available. Only applies to cluster jobmodes |
--maxjobs <NUM> | Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes |
--jobinterval <NUM> | Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult https://support.10xgenomics.com/ for an example override file |
--output-dir <PATH> | Output the results to this directory |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
--custom-bin-size <NUM> | Bin Visium HD data to the specified bin size in addition to the standard binning size (2 µm, 8 µm, 16 µm). Also produces a Loupe file and secondary analysis outputs at the specified bin size in addition to the standard analysis bin size (8 µm) if it is larger than 8 µm. Supply a value in microns. Only even integer values between 4 and 100 are allowed. |
-h, --help | Print help (see a summary with '-h') |
Aggregate data from multiple spaceranger count runs. Visium HD not supported in this release.
Usage:
spaceranger aggr [OPTIONS] --id <ID> --csv <CSV>
| Option | Description |
|---|---|
-h, --help | Print help information |
-V, --version | Print version information |
--id <ID> | A unique run id and output folder name [a-zA-Z0-9_-]+ |
--description <TEXT> | Sample description to embed in output files (default: ) |
--csv <CSV> | Path of CSV file enumerating spaceranger count outputs |
--normalize <MODE> | Library depth normalization mode (default: mapped; possible values: mapped, none) |
--dry | Do not execute the pipeline. Generate an pipeline invocation (.mro) file and stop |
--jobmode <MODE> | Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more details on configuring the pipeline to use a compute cluster (default: local) |
--localcores <NUM> | Set max cores the pipeline may request at one time. Only applies to local jobs |
--localmem <NUM> | Set max GB the pipeline may request at one time. Only applies to local jobs |
--localvmem <NUM> | Set max virtual address space in GB for the pipeline. Only applies to local jobs |
--mempercore <NUM> | Reserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at least this much memory available. Only applies to cluster jobmodes |
--maxjobs <NUM> | Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes |
--jobinterval <NUM> | Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult https://support.10xgenomics.com/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
Run Illumina demultiplexer on sample sheets that contain 10x-specific sample index sets, and generate 10x-specific quality metrics after the demultiplex. Any bcl2fastq argument will work (except a few that are set by the pipeline to ensure proper trimming and sample indexing). The FASTQ output generated will be the same as when running bcl2fastq directly.
These bcl2fastq arguments are overridden by this pipeline:
--fastq-cluster-count--minimum-trimmed-read-length--mask-short-adapter-reads
Usage:
spaceranger mkfastq --run=PATH [options]
spaceranger mkfastq -h | --help | --version
| Option | Description |
|---|---|
--run=PATH | Path of Illumina BCL run folder (required). |
--id=NAME | Name of the folder created by mkfastq. If not supplied, will default to the name of the flowcell referred to by the --run argument. |
--csv=PATH OR --samplesheet=PATH OR --sample-sheet=PATH | Path to the sample sheet. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet. Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12). |
--simple-csv=PATH | Deprecated. Same meaning as --csv. |
--force-single-index | If 10x-supplied i7/i5 paired indices are specified, but the flowcell was run with only one sample index, allow the demultiplex to proceed using the i7 half of the sample index pair. |
--filter-single-index | Only demultiplex samples identified by an i7-only sample index, ignoring dual-indexed samples. Dual-indexed samples will not be demultiplexed. |
--filter-dual-index | Only demultiplex samples identified by i7/i5 dual-indices (e.g., SI-TT-A6), ignoring single-index samples. Single-index samples will not be demultiplexed. |
--rc-i2-override=BOOL | Indicates if the bases in the I2 read are emitted as reverse complement by the sequencing workflow. Set to 'true' for the Reverse Complement Workflow (Workflow B)/ NovaSeq Reagent Kit v1.5 or greater. Set to 'false' for the Forward Strand Workflow (Workflow A) / older NovaSeq Reagent Kits. NOTE: this parameter is autodetected and should only be passed in special circumstances. |
--delete-undetermined | Delete the Undetermined FASTQ files left by bcl2fastq. Useful if your sample sheet is only expected to match a subset of the flowcell. |
--output-dir=PATH | Same as in bcl2fastq. Folder where FASTQs, reports and stats will be generated. |
--project=NAME | Custom project name, to override the samplesheet or to use in conjunction with the --csv argument. |
--jobmode=MODE | Job manager to use. Valid options: local (default), sge, lsf, or a .template file |
--localcores=NUM | Set max cores the pipeline may request at one time. Only applies to local jobs. |
--localmem=NUM | Set max GB the pipeline may request at one time. Only applies to local jobs. |
--localvmem=NUM | Set max virtual address space in GB for the pipeline. Only applies to local jobs. |
--mempercore=NUM | Reserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at least this much memory available. Only applies in cluster jobmodes. |
--maxjobs=NUM | Set max jobs submitted to cluster at one time. Only applies in cluster jobmodes. |
--jobinterval=NUM | Set delay between submitting jobs to cluster, in ms. Only applies in cluster jobmodes. |
--overrides=PATH | The path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult the 10x support website for an example override file. |
--uiport=PORT | Serve web UI at http://localhost:PORT |
--disable-ui | Do not serve the UI. |
--noexit | Keep web UI running after pipestance completes or fails. |
--nopreflight | Skip preflight checks. |
-h --help | Show this message. |
--version | Show version. |
Execute the count pipeline on a small test dataset.
Usage:
spaceranger testrun [OPTIONS] --id <ID>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name [a-zA-Z0-9_-]+ |
--description <TEXT> | Sample description to embed in output files |
--dry | Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop |
--no-internet | Set this if no internet connection is available on the processing computer/node/HPC |
--jobmode <MODE> | Job manager to use. Valid options: local(default), sge, lsf, slurm or path to a .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more details on configuring the pipeline to use a compute cluster (default: local) |
--localcores <NUM> | Set max cores the pipeline may request at one time. Only applies to local jobs |
--localmem <NUM> | Set max GB the pipeline may request at one time.Only applies to local jobs |
--localvmem <NUM> | Set max virtual address space in GB for the pipeline. Only applies to local jobs |
--mempercore <NUM> | Reserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at least this much memory available. Only applies to cluster jobmodes |
--maxjobs <NUM> | Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes |
--jobinterval <NUM> | Set delay between submitting jobs to cluster, inms. Only applies to cluster jobmodes |
--overrides <PATH> | The path to a JSON file that specifiesstage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult https://support.10xgenomics.com/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
--help | Print help information |
Tool for converting feature-barcode matrices from sparse format to dense.
Usage:
mat2csv <input_path> <output_csv> [--genome=GENOME]
mat2csv -h | --help | --version
| Option | Description |
|---|---|
input_path | Path to a Space Ranger feature-barcode matrix. Can be either a feature-barcode h5 file (recommended) or a path to a MEX Space Ranger output folder. |
output_csv | Output CSV file |
--genome=GENOME | Specify which genome to extract. This only applies to multi-genome h5 input files. |
--help | Show this message. |
--version | Show version. |
Prepare a reference for use with 10x analysis software. Requires a GTF and FASTA.
Usage:
spaceranger mkref [OPTIONS] --genome <GENOME_NAMES> --fasta <FASTA_FILES> --genes <GTF_FILES>
| Option | Description |
|---|---|
--genome <GENOME_NAMES> | Unique genome name, used to name output folder [a-zA-Z0-9_-]+. Specify multiple genomes by specifying this argument multiple times; the output folder will be <name1> and <name2> |
--fasta <FASTA_FILES> | Path to FASTA file containing your genome reference. Specify multiple genomes by specifying this argument multiple times |
--genes <GTF_FILES> | Path to genes GTF file containing annotated genes for your genome reference. Specify multiple genomes by specifying this argument multiple times |
--nthreads <NUM_THREADS> | Number of threads used during STAR genome index generation. Defaults to 1 |
--memgb <MEM_GB> | Maximum memory (GB) used. Defaults to 16 |
--ref-version <REF_VERSION> | Optional reference version string to include with reference |
--dry | Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop |
--jobmode <MODE> | Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more details on configuring the pipeline to use a compute cluster (default: local) |
--localcores <NUM> | Set max cores the pipeline may request at one time. Only applies to local jobs |
--localmem <NUM> | Set max GB the pipeline may request at one time. Only applies to local jobs |
--localvmem <NUM> | Set max virtual address space in GB for the pipeline. Only applies to local jobs |
--mempercore <NUM> | Reserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at least this much memory available. Only applies to cluster jobmodes |
--maxjobs <NUM> | Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes |
--jobinterval <NUM> | Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult https://support.10xgenomics.com/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
--help | Print help information |
Genes GTF tool for 10x Genomics Space Ranger. Filter user-supplied GTF files for use as a Space Ranger-compatible genes files for mkref tool.
Usage:
mkgtf <input_gtf> <output_gtf> [--attribute=KEY:VALUE...]
mkgtf -h | --help | --version
| Option | Description |
|---|---|
input_gtf | Path to input genes GTF file. |
output_gtf | Path to filtered output genes GTF file. |
--attribute=<key:value> | Key-value pair in attributes field to be kept in the GTF file. |
--help | Show this message. |
--version | Show version. |
Upload a file to the 10x Genomics support team.
Usage:
spaceranger upload <your_email> <file>
Check your system to check for compatibility with Space Ranger system requirements.
Usage: sitecheck sitecheck -h | --help | --version
| Option | Description |
|---|---|
--help | Show this message. |
--version | Show version. |