Difference between revisions of "HPC:CellRanger"

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[asrini@node156 ~]$ module load cellranger/5.0.1  
 
[asrini@node156 ~]$ module load cellranger/5.0.1  
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[asrini@node156 ~]$ cellranger  
 
[asrini@node156 ~]$ cellranger  
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     help                Prints this message or the help of the given subcommand(s)
 
     help                Prints this message or the help of the given subcommand(s)
  
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[asrini@node156 ~]$ cellranger  -V
 
[asrini@node156 ~]$ cellranger  -V
 
cellranger cellranger-5.0.1
 
cellranger cellranger-5.0.1

Revision as of 19:05, 26 January 2021

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


Submitting Cell Ranger Jobs

Other Pages