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 Single Cell 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 |
upload | Upload analysis logs to 10x Genomics support |
sitecheck | Collect linux system configuration information |
| 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 [FLAGS] [OPTIONS] --id <ID> --reference <PATH> --libraries <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 |
--reference <PATH> | Path to folder containing cellranger-arc-compatible reference. Reference packages can be downloaded from www.10xgenomics.com/support or constructed using the cellranger-arc mkref command |
--libraries <CSV> | Path to 3-column CSV file defining the paths to ATAC and gene expression FASTQ data generated with the Chromium Single Cell Multiome ATAC + Gene Expression solution. A template CSV would look as follows (blank lines are ignored): fastqs,sample,library_type /data/HAWT7ADXX/outs/fastq_path,myATAC,Chromatin Accessibility /data/H35KCBCXY/outs/fastq_path,myGEX,Gene Expression |
--min-atac-count <NUM> | Cell caller override: define the minimum number of ATAC transposition events in peaks (ATAC counts) 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 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 |
--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 www.10xgenomics.com/support 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://www.10xgenomics.com/support/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
| Flag | Description |
|---|---|
--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 |
--no-bam | Do not generate bam files |
--dry | Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
-h, --help | Prints help information |
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: 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 [FLAGS] [OPTIONS] --id <ID> --reference <PATH> --csv <CSV>
| Flag | Description |
|---|---|
--nosecondary | Disable secondary analysis, e.g. clustering |
--dry | Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
-h, --help | Prints help information |
| 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 www.10xgenomics.com/support 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. For example, a CSV for aggregating two samples would look as follows (blank lines are ignored): library_id,atac_fragments,per_barcode_metrics,gex_molecule_info L1,/data/L1/outs/atac_fragments.tsv.gz,/data/L1/outs/per_barcode_metrics.csv,/data/L1/outs/gex_molecule_info.h5 L2,/data/L2/outs/atac_fragments.tsv.gz,/data/L2/outs/per_barcode_metrics.csv,/data/L2/outs/gex_molecule_info.h5 Optionally, metadata associated with these libraries can be specified using additional columns. This information is not used by the pipeline but will be available in the Loupe file for visualization. |
--peaks <BED> | Override peak caller: specify peaks to use in downstream analyses from 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] |
--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 www.10xgenomics.com/support 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://www.10xgenomics.com/support/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
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 [FLAGS] [OPTIONS] --id <ID> --reference <PATH> --matrix <H5> --atac-fragments <TSV.GZ>
| Flag | Description |
|---|---|
--dry | Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop |
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
-h, --help | Prints help information |
| 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 www.10xgenomics.com/support 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. If you intend to subset to a set of barcodes then use the raw matrix, 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: any subset of random_seed, k_means_max_clusters, feature_linkage_max_dist_mb, num_gex_pcs, num_atac_pcs. For example, to override the number of GEX principal components used to 15 and the distance threshold for feature linkage computation to 2.5 megabases, the CSV would take the form (blank lines are ignored): num_gex_pcs,15 feature_linkage_max_dist_mb,2.5 |
--barcodes <CSV> | Specify barcodes to use in analysis. The barcodes could be specified in a text file that contains one barcode per line, like this (blank lines are ignored): ACGT-1 TGCA-1 Or you can supply a CSV (with/without a header) whose first column will be used - exports from Loupe Browser will have this format. For example, Barcode,Cluster ACGT-1,T cells TGCA-1,B cells |
--min-atac-count <NUM> | Cell caller override: define the minimum number of ATAC transposition events in peaks (ATAC counts) 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 secondary analyses from 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', it's possible to pass the same aggregation CSV in order to retain per-library tag information in the resulting .cloupe file |
--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 www.10xgenomics.com/support 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://www.10xgenomics.com/support/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
Run a tiny cellranger-arc count pipeline to verify software integrity.
Usage: cellranger-arc testrun [FLAGS] [OPTIONS] --id <ID>
| Flag | Description |
|---|---|
--disable-ui | Do not serve the web UI |
--noexit | Keep web UI running after pipestance completes or fails |
--nopreflight | Skip preflight checks |
-h, --help | Prints help information |
| 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 path to a .template file. Search for help on "Cluster Mode" at www.10xgenomics.com/support 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://www.10xgenomics.com/support/ for an example override file |
--uiport <PORT> | Serve web UI at http://localhost:PORT |
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. |
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