The cellranger mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate Cell Ranger-compatible FASTQ files.
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 |
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 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 |
--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 |
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-atac mkfastq --run=PATH [options]
cellranger-atac mkfastq -h | --help | --version
Required:
| 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 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. |
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/single-cell-atac/software |
--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