This page lists the most commonly used Cell Ranger pipelines and commands. For the full list of commands, subcommands, run cellranger --help.
Usage: cellranger count [OPTIONS] --id <ID> --create-bam <true|false>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files (default: ) |
--transcriptome <PATH> | Path of folder containing 10x-compatible transcriptome reference |
--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, declaring Feature Barcode constructs and associated barcodes |
--expect-cells <NUM> | Expected number of recovered cells, used as input to cell calling algorithm |
--force-cells <NUM> | Force pipeline to use this number of cells, bypassing cell calling algorithm. (MINIMUM: 10) |
--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 |
--include-introns <true/false> | Include intronic reads in count (default: true) (possible values: true, false) |
--chemistry <CHEM> | Assay configuration. NOTE: by default the assay configuration is detected automatically, which is the recommended mode. You usually will not need to specify a chemistry. Options are: auto for autodetection, threeprime for Single Cell 3', fiveprime for Single Cell 5', SC3Pv1 or SC3Pv2 or SC3Pv3 or SC3Pv4 for Single Cell 3' v1/v2/v3/v4, SC3Pv3LT for Single Cell 3' v3 LT, SC3Pv3HT for Single Cell 3' v3 HT, SC5P-PE or SC5P-PE-v3 or SC5P-R2 or SC5P-R2-v3 for Single Cell 5', paired-end/R2-only, SC-FB for Single Cell Antibody-only 3' v2 or 5'. To analyze the GEX portion of multiome data, chemistry must be set to ARC-v1 (default: auto) |
--no-libraries | Proceed with processing using a --feature-ref but no Feature Barcode libraries specified with the libraries flag |
--check-library-compatibility <true/false> | Whether to check for barcode compatibility between libraries. (default: true) (possible values: true, false) |
--tenx-cloud-token-path <PATH> | The path to the 10x Cloud Analysis user token used to enable cell annotation. If not provided, will default to the location stored through cellranger cloud auth setup |
--cell-annotation-model <MODEL> | Cell annotation model to use. Valid model names can be viewed by running cellranger cloud annotation models or on the 10x Genomics Support site (https://www.10xgenomics.com/support). If "auto", uses the default model for the species. If not provided, does not run cell annotation |
--min-crispr-umi <NUM> | Minimum CRISPR UMI threshold (default: 3) |
--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 |
--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 |
Usage: cellranger multi [OPTIONS] --id <ID> --csv <CSV>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files (default: ) |
--csv <CSV> | Path of CSV file enumerating input libraries and analysis parameters |
--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 |
--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://10xgen.com/resource-override 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 |
-h, --help | Print help |
Usage: cellranger multi-template [OPTIONS]
| Option | Description |
|---|---|
-o, --output <CSV> | Optional output file path |
-p, --parameters | Print multi config parameter options and descriptions |
-h, --help | Print help |
Usage: cellranger vdj [OPTIONS] --id <ID> --fastqs <PATH>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files (default: ) |
--reference <PATH> | Path of folder containing 10x-compatible VDJ reference. Optional if --denovo is specified |
--fastqs <PATH> | Path to input FASTQ data |
--project <TEXT> | Name of the project folder within a mkfastq or bcl2fastq-generated folder to pick FASTQs from |
--sample <PREFIX> | Prefix of the filenames of FASTQs to select |
--lanes <NUMS> | Only use FASTQs from selected lanes |
--denovo | Run in reference-free mode (do not use annotations) |
--chain <CHAIN_SPEC> | Chain type to display metrics for: TR for T cell receptors, IG for B cell receptors, or auto to autodetect (default: auto) |
--inner-enrichment-primers <PATH> | If inner enrichment primers other than those provided in the 10x kits are used, they need to be specified here as a textfile with one primer per line. Disable secondary analysis, e.g. clustering |
--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 |
--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://10xgen.com/resource-override 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 |
-h, --help | Print help |
Usage: cellranger aggr [OPTIONS] --id <ID> --csv <CSV>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files (default: ) |
--csv <CSV> | Path of CSV file enumerating cellranger count/vdj/multi outputs |
--normalize <MODE> | Library depth normalization mode (default: mapped) (possible values: mapped, none) |
--nosecondary | Disable secondary analysis, e.g. clustering |
--dry | Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop |
--min-crispr-umi <NUM> | Minimum CRISPR UMI threshold (default: 3) |
--enable-tsne <true|false> | Enable t-SNE projection (default: false) (possible values: true, false) |
--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 |
--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://10xgen.com/resource-override 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 |
-h, --help | Print help |
Usage: cellranger annotate [OPTIONS] --id <ID> --matrix <MATRIX_H5>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files (default: ) |
--tenx-cloud-token-path <PATH> | Path to 10x Cloud cell annotation token file |
--cell-annotation-model <CELL_ANNOTATION_MODEL> | Cell annotation model to use |
--cloupe <CLOUPE> | Cloupe file to use |
--cloupe-group-name <TEXT> | Name of track to add onto the cloupe file |
--matrix <MATRIX_H5> | A feature-barcode matrix containing data for one genome. Should be the filtered version |
--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 |
--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://10xgen.com/resource-override 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 |
-h, --help | Print help |
Usage: cellranger reanalyze [OPTIONS] --id <ID> --matrix <MATRIX_H5>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name |
--description <TEXT> | Sample description to embed in output files (default: ) |
--matrix <MATRIX_H5> | A feature-barcode matrix containing data for one genome. Should be the filtered version, unless using --force-cells |
--params <PARAMS_CSV> | A CSV file specifying analysis parameters. Optional |
--barcodes <BARCODES_CSV> | A CSV file containing a list of cell barcodes to use for reanalysis, e.g. barcodes exported from Loupe Browser. Optional |
--genes <GENES_CSV> | A CSV file containing a list of feature IDs to use for reanalysis. For gene expression, this should correspond to the gene_id field in the reference GTF should be (e.g. ENSG... for ENSEMBL-based references). Optional |
--exclude-genes <GENES_CSV> | A CSV file containing a list of feature IDs to exclude from reanalysis. For gene expression, this should correspond to the gene_id field in the reference GTF (e.g., ENSG... for ENSEMBL-based references). The exclusion is applied after --genes. Optional |
--agg <AGGREGATION_CSV> | If the input matrix was produced by 'aggr', you may pass the same aggregation CSV in order to retain per-library tag information in the resulting .cloupe file. This argument is required to enable chemistry batch correction. Optional |
--force-cells <NUM> | Force pipeline to use this number of cells, bypassing cell calling algorithm. (MINIMUM: 10) |
--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 |
--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://10xgen.com/resource-override 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 |
-h, --help | Print help |