Dockerized Cell Ranger v8.0.0
- GEX: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.0/
- VDJ: https://support.10xgenomics.com/single-cell-vdj/software/downloads/7.0/
Version 7.2 supports Flex + CITE, Version 8.0 supports Visium HD.
The code is available to everyone under the standard MIT license. However, the code internally uses 10x software, so please make sure that you read and agree to 10x End User Software License.
SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/) is required for smooth and uninteruppted build process (e.g. CI/CD). For setup, please refer to this page. All the instructions below is given under the assumption that you have already configured SCING in your environment.
SCING installation is required.
conda activate scing
./build.shconda activate scing
./push.sh$ cellranger --help
cellranger cellranger-8.0.0
Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data
USAGE:
cellranger <SUBCOMMAND>
OPTIONS:
-h, --help Print help information
-V, --version Print version information
SUBCOMMANDS:
count Count gene expression (targeted or whole-transcriptome) and/or feature
barcode reads from a single sample and GEM well
multi Analyze multiplexed data or combined gene expression/immune
profiling/feature barcode data
vdj Assembles single-cell VDJ receptor sequences from 10x Immune Profiling
libraries
aggr Aggregate data from multiple Cell Ranger runs
reanalyze Re-run secondary analysis (dimensionality reduction, clustering, etc)
targeted-compare Analyze targeted enrichment performance by comparing a targeted sample
to its cognate parent WTA sample (used as input for targeted gene
expression)
targeted-depth Estimate targeted read depth values (mean reads per cell) for a
specified input parent WTA sample and a target panel CSV file
mkvdjref Prepare a reference for use with CellRanger VDJ
mkfastq Run Illumina demultiplexer on sample sheets that contain 10x-specific
sample index sets
testrun Execute the 'count' pipeline on a small test dataset
mat2csv Convert a gene count matrix to CSV format
mkref Prepare a reference for use with 10x analysis software. Requires a GTF
and FASTA
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
help Print this message or the help of the given subcommand(s)$ cellranger count --help
cellranger-count
Count gene expression (targeted or whole-transcriptome) and/or feature barcode reads from a single
sample and GEM well
USAGE:
cellranger count [OPTIONS] --id <ID> --transcriptome <PATH>
OPTIONS:
--id <ID>
A unique run id and output folder name [a-zA-Z0-9_-]+
--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
--target-panel <CSV>
The target panel CSV file declaring the target panel used, if any. Default analysis will
exclude intronic mapped reads, which is the recommended mode for targeted assay. Use
include-introns=true to include intronic mapped reads in analysis
--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]
--no-bam
Set --no-bam to not generate the BAM file. This will reduce the total computation time
for the pipestance and the size of the output directory. If unsure, we recommend not to
use this option. BAM file could be useful for troubleshooting and downstream analysis
--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 unless --target-panel is specified in
which case default=false)
--chemistry <CHEM>
Assay configuration. NOTE: by default the assay configuration is detected automatically,
which is the recommened 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' for Single Cell 3' v1/v2/v3, 'SC3Pv3LT' for
Single Cell 3' v3 LT, 'SC3Pv3HT' for Single Cell 3' v3 HT, 'SC5P-PE' or 'SC5P-R2' for
Single Cell 5', paired-end/R2-only, 'SC-FB' for Single Cell Antibody-only 3' v2 or 5'
[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]
--no-target-umi-filter
Turn off the target UMI filtering subpipeline. Only applies when --target-panel is used
--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 [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://support.10xgenomics.com/ 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$ cellranger vdj --help
cellranger-vdj
Assembles single-cell VDJ receptor sequences from 10x Immune Profiling libraries
USAGE:
cellranger vdj [OPTIONS] --id <ID> --fastqs <PATH>
OPTIONS:
--id <ID>
A unique run id and output folder name [a-zA-Z0-9_-]+
--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 [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://support.10xgenomics.com/ 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