cellranger

Version:: 7.0.0, 9.0.1
Category:: bio
Cluster:: Loki

Author / Distributor

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Description

Genomics 10X Cellranger 7.0.0 module is a set of analysis tool pipelines that willprocess Chromium single-cell data to aligned reads, and generate a feature rich barcode matrix, clustering groups and other secondary analsys files. Cellranger module requires the module bcl2fastq2 2.20.0 to run “cellranger mkfastq”. Raw Data as a BCL file must be from RTA sequencers version 1.18.94 or newer

Documentation

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)

Examples/Usage

List cellranger modules:
```
$ module avail cellranger
```
Load the Cellranger module:
```
$ module load bio/CellRanger/7.0.0
```
Check the loaded modules:
```
$ module list
```
Unload the Cellranger module:
```
$ module unload bio/CellRanger/7.0.0
```

Installation

Source code is obtained from CellRanger