Contents
Cell Ranger
Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Note: At present, we are not providing References for any species. HPC users will have to download and build these as needed.
Usage
Cell Ranger has different pipelines intended for different experiments. It is recommended that HPC users read the Cell Ranger documentation, available here, for details on the available pipelines and the various command options before reading this section of our wiki.
The sections below describe how to run Cell Ranger on our HPC system.
Running Cell Ranger in an Interactive Session
To run Cell Ranger in an interactive session see same usage below (click "expand")
[asrini@node156 ~]$ module show cellranger/5.0.1 ------------------------------------------------------------------- /usr/share/Modules/modulefiles/cellranger/5.0.1: module-whatis Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. prepend-path PATH /opt/software/cellranger/5.0.1/bin -------------------------------------------------------------------
[asrini@node156 ~]$ module load cellranger/5.0.1
[asrini@node156 ~]$ cellranger
cellranger cellranger-5.0.1
Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data
USAGE:
cellranger <SUBCOMMAND>
FLAGS:
-h, --help Prints help information
-V, --version Prints 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 gene expression (targeted or whole-transcriptome) and/or feature barcode and/or immune profiling data from a single sample and GEM well
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 Prints this message or the help of the given subcommand(s)
[asrini@node156 ~]$ cellranger -V
cellranger cellranger-5.0.1
