For a list of subcommands, run cellranger-arc --help.
Usage:
cellranger-arc <SUBCOMMAND>
cellranger-arc --help
| Subcommand | Description |
|---|---|
count | Count ATAC and gene expression reads from a single library |
mkfastq | Run bcl2fastq on Epi Multiome ATAC + Gene Expression sequencing data |
mkref | Create a cellranger-arc-compatible reference package |
aggr | Aggregate data from multiple cellranger-arc count runs |
reanalyze | Re-run secondary analysis (dimensionality reduction, clustering, feature linkage etc.) on a completed cellranger-arc count or cellranger-arc aggr run |
testrun | Run a tiny cellranger-arc count pipeline to verify software integrity |
mkgtf | Filter a GTF file by attribute prior to creating a 10x reference |
cloud | Invoke cloud commands |
upload | Upload analysis logs to 10x Genomics support |
sitecheck | Collect linux system configuration information |
telemetry | Configure and inspect telemetry settings and data |
| Flags | Description |
|---|---|
-h, --help | Prints help information |
-V, --version | Prints version information |
Count ATAC and gene expression reads from a single library.
Usage: cellranger-arc count [OPTIONS] --id <ID> --reference <PATH> --libraries <CSV> --create-bam <true|false>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name [a-zA-Z0--9_-]+ of maximum length 64 characters. |
--description <TEXT> | Sample description to embed in output files. |
--reference <PATH> | Path to folder containing cellranger-arc-compatible reference. Reference packages can be downloaded from support.10xgenomics.com or constructed using the cellranger-arc mkref command. |
--libraries <CSV> | Path to a 3-column CSV file defining the paths to ATAC and gene expression FASTQ data. |
--min-atac-count <NUM> | Cell caller override: define the minimum number of ATAC transposition events in peaks for a cell barcode. Note: this option must be specified in conjunction with min-gex-count. With --min-atac-count=X and --min-gex-count=Y a barcode is defined as a cell if it contains at least X ATAC counts AND at least Y GEX UMI counts. |
--min-gex-count <NUM> | Cell caller override: define the minimum number of GEX UMI counts for a cell barcode. Note: this option must be specified in conjunction with min-atac-count. With --min-atac-count=X and --min-gex-count=Y a barcode is defined as a cell if it contains at least X ATAC counts AND at least Y GEX UMI counts. |
--peaks <BED> | Override peak caller: specify peaks to use in downstream analyses from a supplied 3-column BED file. The supplied peaks file must be sorted by position and not contain overlapping peaks; comment lines beginning with # are allowed. |
--gex-exclude-introns | Disable counting of intronic reads. In this mode, only reads that are exonic and compatible with annotated splice junctions in the reference are counted. Note: using this mode will reduce the UMI counts in the feature-barcode matrix. |
--tenx-cloud-token-path <PATH> | The path to the 10x Cloud Analysis user token used to enable cell annotation. If not provided, it will default to the location stored through the cellranger-arc cloud auth setup. |
--cell-annotation-model <MODEL> | Cell annotation model to use. Valid model names can be viewed by running cellranger-arc cloud annotation models or on the 10x Genomics Support site. If "auto", it uses the default model for the species. If not provided, cell annotation is not run. |
--create-bam <true/false> | Enable or disable BAM file generation. Setting --create-bam=false reduces computation time and output directory size. We recommend setting --create-bam=true if unsure. See https://10xgen.com/create-bam for guidance. [possible values: true, false] |
--nosecondary | Disable secondary analysis, e.g., clustering. |
--rna-r1-length <NUM> | Trim the input Read 1 for GEX data to this length before analysis. |
--rna-r2-length <NUM> | Trim the input Read 2 for GEX data to this length before analysis. |
--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 a path to a .template file. Search for "Cluster Mode" at support.10xgenomics.com for details. |
--localcores <NUM> | Set the max cores the pipeline may request at one time. Only applies to local jobs. |
--localmem <NUM> | Set the max GB the pipeline may request at one time. Only applies to local jobs. |
--localvmem <NUM> | Set the 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. Only applies to cluster jobmodes. |
--maxjobs <NUM> | Set the max jobs submitted to the cluster at one time. Only applies to cluster jobmodes. |
--jobinterval <NUM> | Set the delay in milliseconds between submitting jobs to the cluster. Only applies to cluster jobmodes. |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. See https://10xgen.com/resource-override for an example. |
--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 the web UI running after the pipestance completes or fails. |
--nopreflight | Skip preflight checks. |
-h, --help | Print help (see a summary with -h). |
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
This pipeline has been deprecated beginning with Cell Ranger ARC v2.1.
Usage: cellranger-arc mkfastq --run=PATH [options] cellranger-arc mkfastq -h | --help | --version
| Option | Description |
|---|---|
--run=PATH | (required) Path of Illumina BCL run folder. |
--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, --samplesheet=PATH, --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 Workflow A / NovaSeq Reagent Kit v1.5 or greater. Set to 'false' for Wokflow B / older NovaSeq Reagent Kits. NOTE: this parameter is autodetected based and should only be passed in special circumstances. |
--lanes=NUMS | Comma-delimited series of lanes to demultiplex. Shortcut for the --tiles argument. |
--use-bases-mask=MASK | Same as bcl2fastq; override the read lengths as specified in RunInfo.xml. See Illumina bcl2fastq documentation for more information. |
--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. |
Reference preparation tool for 10x Genomics Cell Ranger Multiome ATAC + Gene Expression. Build a reference package from a user-supplied genome FASTA and gene GTF file. Creates a new folder named after the genome. NOTE: Multi-species references are not supported by cellranger-arc. If you construct a multi-species reference and run cellranger-arc count you will not be able to generate all the outputs of the pipeline.
Usage: cellranger-arc mkref --config=PATH [options] mkref -h | --help | --version
| Option | Description |
|---|---|
--config | (required) Path to configuration file containing additional information about the reference. See online documentation for more details.Path to configuration file containing additional information about the reference. See online documentation for more details. |
--nthreads=<num> | Number of threads used during STAR genome index generation. Defaults to 1. |
--memgb=<num> | Maximum memory (GB) used when aligning reads with STAR. Defaults to 16. |
--ref-version=<str> | Optional reference version string to include with reference. |
-h --help | Show this message. |
--version | Show version. |
Aggregate data from multiple cellranger-arc count runs.
Usage: cellranger-arc aggr [OPTIONS] --id <ID> --reference <PATH> --csv <CSV>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name [a-zA-Z0-9_-]+ of maximum length 64 characters. |
--description <TEXT> | Sample description to embed in output files. [default: ] |
--reference <PATH> | Path to folder containing cellranger-arc-compatible reference. Reference packages can be downloaded from support.10xgenomics.com or constructed using the cellranger-arc mkref command. Note: this reference must match the reference used for the initial cellranger-arc count run. |
--csv <CSV> | Path to CSV file enumerating 'cellranger-arc count' outputs required for aggregation. |
--peaks <BED> | Override peak caller: specify peaks to use in downstream analyses from a supplied 3-column BED file. The supplied peaks file must be sorted by position and not contain overlapping peaks; comment lines beginning with # are allowed. |
--normalize <MODE> | Library depth normalization mode. [default: depth] [possible values: none, depth] |
--nosecondary | 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 a path to a .template file. Search for "Cluster Mode" at support.10xgenomics.com for details. |
--localcores <NUM> | Set the max cores the pipeline may request at one time. Only applies to local jobs. |
--localmem <NUM> | Set the max GB the pipeline may request at one time. Only applies to local jobs. |
--localvmem <NUM> | Set the 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. Only applies to cluster jobmodes. |
--maxjobs <NUM> | Set the max jobs submitted to the cluster at one time. Only applies to cluster jobmodes. |
--jobinterval <NUM> | Set the delay in milliseconds between submitting jobs to the cluster. Only applies to cluster jobmodes. |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. See https://10xgen.com/resource-override for an example. |
--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 the web UI running after the pipestance completes or fails. |
--nopreflight | Skip preflight checks. |
-h, --help | Print help (see a summary with -h). |
Re-run secondary analysis (dimensionality reduction, clustering, feature linkage etc.) on a completed cellranger-arc count or cellranger-arc aggr run.
Usage: cellranger-arc reanalyze [OPTIONS] --id <ID> --reference <PATH> --matrix <H5> --atac-fragments <TSV.GZ>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name [a-zA-Z0-9_-]+ of maximum length 64 characters. |
--description <TEXT> | Sample description to embed in output files. [default: ] |
--reference <PATH> | Path to folder containing cellranger-arc-compatible reference. Reference packages can be downloaded from support.10xgenomics.com or constructed using the cellranger-arc mkref command. Note: this reference must match the reference used for the initial cellranger-arc count run. |
--matrix <H5> | Path to a feature barcode matrix H5 generated by cellranger-arc count or aggr. Use the raw matrix if you intend to subset barcodes, otherwise use the filtered feature barcode matrix. |
--atac-fragments <TSV.GZ> | Path to the atac_fragments.tsv.gz generated by cellranger-arc count or aggr. Note: it is assumed that the tabix index file atac_fragments.tsv.gz.tbi is present in the same directory. |
--params <CSV> | Specify key-value pairs in CSV format for analysis. |
--barcodes <CSV> | Specify barcodes to use in analysis from a text file (one barcode per line) or a CSV file (first column is used). |
--min-atac-count <NUM> | Cell caller override: define the minimum number of ATAC transposition events in peaks for a cell barcode. Must be specified with --min-gex-count. |
--min-gex-count <NUM> | Cell caller override: define the minimum number of GEX UMI counts for a cell barcode. Must be specified with --min-atac-count. |
--peaks <BED> | Override peak caller: specify peaks to use in secondary analyses from a supplied 3-column BED file. The supplied peaks file must be sorted by position and not contain overlapping peaks; comment lines beginning with # are allowed. |
--agg <AGGREGATION_CSV> | If the input matrix was produced by cellranger-arc aggr, pass the same aggregation CSV to retain per-library tag information in the resulting .cloupe file. |
--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 a path to a .template file. Search for "Cluster Mode" at support.10xgenomics.com for details. |
--localcores <NUM> | Set the max cores the pipeline may request at one time. Only applies to local jobs. |
--localmem <NUM> | Set the max GB the pipeline may request at one time. Only applies to local jobs. |
--localvmem <NUM> | Set the 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. Only applies to cluster jobmodes. |
--maxjobs <NUM> | Set the max jobs submitted to the cluster at one time. Only applies to cluster jobmodes. |
--jobinterval <NUM> | Set the delay in milliseconds between submitting jobs to the cluster. Only applies to cluster jobmodes. |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. See https://10xgen.com/resource-override for an example. |
--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. |
Run a tiny cellranger-arc count pipeline to verify software integrity.
Usage: cellranger-arc testrun [OPTIONS] --id <ID>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name [a-zA-Z0-9_-]+ of maximum length 64 characters. |
--description <TEXT> | Sample description to embed in output files. |
--jobmode <MODE> | Job manager to use. Valid options: local (default), sge, lsf, slurm or a path to a .template file. See support.10xgenomics.com for details on cluster configuration. |
--localcores <NUM> | Set the max cores the pipeline may request at one time. Only applies to local jobs. |
--localmem <NUM> | Set the max GB the pipeline may request at one time. Only applies to local jobs. |
--localvmem <NUM> | Set the 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 is available. Only applies to cluster jobmodes. |
--maxjobs <NUM> | Set the max jobs submitted to the cluster at one time. Only applies to cluster jobmodes. |
--jobinterval <NUM> | Set the delay in milliseconds between submitting jobs to the cluster. Only applies to cluster jobmodes. |
--overrides <PATH> | The path to a JSON file that specifies stage-level overrides for cores and memory. See https://10xgen.com/resource-override for an example. |
--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 the web UI running after the pipestance completes or fails. |
--nopreflight | Skip preflight checks. |
-h, --help | Print help. |
Genes GTF tool for 10x Genomics Cell Ranger Multiome ATAC + Gene Expression. Filter user-supplied GTF files for use as Cell Ranger Multiome ATAC + Gene Expression-compatible genes files for mkref tool.
Usage: mkgtf <input_gtf> <output_gtf> [--attribute=KEY:VALUE...]
mkgtf -h | --help | --version
| Argument | Description |
|---|---|
input_gtf | Path to input genes GTF file. |
output_gtf | Path to filtered output genes GTF file. |
| Option | Description |
|---|---|
--attribute=<key:value> | Key-value pair in attributes field to be kept in the GTF file. |
-h --help | Show this message. |
--version | Show version. |
The official command-line client for 10x Genomics Cloud Analysis.
You can use txg help [command] for more information on any of the available
commands.
Before using the CLI, you will need to authenticate with txg auth setup. See
txg help auth for more information, or visit https://support.10xgenomics.com/cloud-analysis
Usage: txg [command]
| Command | Description |
|---|---|
analyses | Manage analyses |
annotation | Cell type annotation functions |
auth | Manage authentication |
fastqs | Upload and manage FASTQs |
files | Upload and manage files |
help | Help about any command |
projects | Manage projects |
references | Upload and manage custom references |
| Flag | Description |
|---|---|
--access-token string | Specify an access token to use. Default: the saved token from txg auth setup. |
-y, --assumeyes | Assume yes (don't interactively prompt for confirmation, etc). Default: off. |
-H, --header header | Extra header to include in HTTP requests. May be given multiple times. Each header must be of the form 'Header: value'. Default: no extra headers. |
-h, --help | Display help and exit. |
-q, --quiet | Don't show progress or messages. Default: off. |
-v, --verbose | Display extra debugging information. Default: off. |
--version | Display version and exit. |
Upload analysis logs to 10x Genomics support.
Usage: cellranger-arc upload <your_email> <file>
Collect Linux system configuration information.
Usage: cellranger-arc sitecheck
cellranger-arc sitecheck -h | --help | --version
Usage: cellranger-arc telemetry [help] (collect|check|disable|enable|list|show)
For more information about what data is collected and how it's used, visit this page
| Command | Description |
|---|---|
collect | Collect telemetry data, if enabled. |
check | Show whether telemetry is currently enabled and configuration information. |
disable | Disable telemetry collection for this user. |
enable | Enable telemetry collection for this user. |
list | List files containing saved telemetry data for this product. |
show | Display contents of saved telemetry data for this product. |