For a list of subcommands, run cellranger-atac --help.
Usage:
cellranger-atac <SUBCOMMAND>
cellranger-atac --help
| Subcommand | Description |
|---|---|
count | Count reads from a single Single Cell ATAC library |
mkfastq | Run bcl2fastq on Single Cell ATAC sequencing data (deprecated) |
mkref | Create a cellranger-atac-compatible reference package |
aggr | Aggregate data from multiple cellranger-atac count runs |
reanalyze | Re-run secondary analysis (dimensionality reduction, clustering, etc) on a completed cellranger-atac count or cellranger-atac aggr run |
testrun | Run a tiny cellranger-atac count pipeline to verify software integrity |
upload | Upload analysis logs to 10x Genomics support |
sitecheck | Collect linux system configuration information |
help | Print this message or the help of the given subcommand(s) |
| Option | Description |
|---|---|
-h, --help | Print help information |
-V, --version | Print version information |
Count reads from a single Single Cell ATAC library.
Usage: cellranger-atac count [OPTIONS] --id <ID> --reference <PATH> --fastqs <PATH>
| 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 a Cell Ranger ATAC or Cell Ranger ARC reference |
--fastqs <PATH> | Path to input FASTQ data |
--project <TEXT> | Name of the project folder to pick FASTQs from |
--sample <PREFIX> | Prefix of the filenames of FASTQs to select |
--lanes <NUMS> | Only use FASTQs from selected lanes |
--force-cells <NUM> | Define the top N barcodes with the most fragments overlapping peaks as cells. N must be a positive integer. Please consult the documentation before using this option |
--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 |
--dim-reduce <STR> | Dimensionality reduction mode for clustering [default: lsa] [possible values: lsa, pca, plsa] |
--nosecondary | Adding --nosecondary to the command disables the generation of secondary analysis results, such as clustering and dimensionality reduction (tSNE/UMAP) and the .cloupe output file. This flag does not require a true or false value to be specified. |
--subsample-rate <FRACTION> | Downsample to preserve this fraction of reads |
--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 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 |
--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 information |
Create a cellranger-atac-compatible reference package.
Usage:
cellranger-atac mkref --config=PATH [options]
cellranger-atac mkref -h | --help | --version
| Option | Description |
|---|---|
--config | Path to configuration file containing additional information about the reference. See online documentation for more details. |
--ref-version=<str> | Optional reference version string to include with reference. |
-h --help | Show this message. |
--version | Show version. |
Aggregate data from multiple cellranger-atac count runs.
Usage: cellranger-atac aggr [OPTIONS] --id <ID> --csv <CSV> --reference <PATH>
| 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: ] |
--csv <CSV> | Path to CSV file enumerating cellranger-atac count outputs. 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. |
--reference <PATH> | Path to folder containing a Cell Ranger ATAC or Cell Ranger ARC reference |
--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: depth, none] |
--nosecondary | Adding --nosecondary to the command disables the generation of secondary analysis results, such as clustering and dimensionality reduction (tSNE/UMAP) and the .cloupe output file. This flag does not require a true or false value to be specified. |
--dim-reduce <STR> | Dimensionality reduction mode for clustering [default: lsa] [possible values: lsa, pca, plsa] |
--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 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 |
--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 information |
Re-run secondary analysis (dimensionality reduction, clustering, etc) on a completed cellranger-atac count or cellranger-atac aggr run.
Usage: cellranger-atac reanalyze [OPTIONS] --id <ID> --peaks <BED> --fragments <TSV.GZ> --reference <PATH>
| Option | Description |
|---|---|
--id <ID> | A unique run id and output folder name [a-zA-Z0-9_-]+ of maximum length 64 characters |
--peaks <BED> | 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 |
--fragments <TSV.GZ> | Path to the fragments.tsv.gz generated by cellranger-atac count or aggr. Note it is assumed that the tabix index file fragments.tsv.gz.tbi is present in the same directory |
--reference <PATH> | Path to folder containing a Cell Ranger ATAC or Cell Ranger ARC reference |
--description <TEXT> | Sample description to embed in output files [default: ] |
--params <PARAMS_CSV> | A CSV file specifying analysis parameters. Please see the following URL for details on the CSV format: www.10xgenomics.com/support/epi-atac/documentation/software-analysis |
--force-cells <NUM> | Define the top N barcodes with the most fragments overlapping peaks as cells. N must be a positive integer less than or equal to 20,000. Please consult the documentation before using this option |
--barcodes <CSV> | Specify barcodes to use in analysis. The barcodes could be specified in a text file that contains one barcode per line, or you can supply a CSV (with/without a header) whose first column will be used - exports from Loupe Browser will have this format. |
--agg <AGGREGATION_CSV> | If the input matrix was produced by cellranger-atac aggr, it is possible to pass the same aggregation CSV in order 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 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 |
--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 information |
Run a tiny cellranger-atac count pipeline to verify software integrity.
Usage: cellranger-atac 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 |
--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 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 |
--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 information |
Upload analysis logs to 10x Genomics support.
Usage: cellranger-atac upload <your_email> <file>
Collect Linux system configuration information.
Usage: cellranger-atac sitecheck