Cell Ranger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.


Steps to create the pre-built Cell Ranger reference packages from the downloads page.

Running Cell Ranger

You don't have to download or install the programm. Just use one of the versions (module available cellranger) installed on the LRZ Linux Cluster.

Open a Terminal, or a Putty session and type:

$ ssh -Y lxlogin(1,2,3,4).lrz.de (-l userID)
$ module use -a /lrz/sys/share/modules/extfiles
$ module load cellranger/3.1.0 (old version: cellranger/2.2.0)

If you type module list you will see that not only cellranger is loaded but also bcl2fastq

Please use salloc for interactive testing


Download some References

How to download the Human reference (GRCh38) dataset required for Cell Ranger.

$ wget  http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-1.2.0.tar.gz
$ tar -xzvf refdata-cellranger-GRCh38-1.2.0.tar.gz

How to submit a Cell Ranger job

Configure, submit and execute serial SLURM jobs. Running mkfastq with an Illumina Experiment Manager sample sheet can be used as example.

Download the tiny-bcl tar file:

$ wget http://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz
$ tar -xzvf cellranger-tiny-bcl-1.2.0.tar.gz

Download the simple CSV layout file and the the Illumina Experiment Manager sample sheet

$ wget http://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv
$ wget http://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv

Download the FASTQ files (73.61 GB) that we will be used by cellranger count as example

$ wget -c -N http://s3-us-west-2.amazonaws.com/10x.files/samples/cell-exp/2.1.0/pbmc8k/pbmc8k_fastqs.tar
$ tar -xf pbmc8k_fastqs.tar

Edit a batch job (e.g.: job_mkfastq.sh) with the editor of preference.

#SBATCH -o /DIR/job_mkfastq.out
#SBATCH -D /DIR/CellRanger
#SBATCH -J job_mkfastq.sh
#SBATCH --get-user-env
#SBATCH --clusters=inter
#SBATCH --partition=teramem_inter
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --mail-type=end
#SBATCH --mail-user=USER@lrz.de # email to receive notifications
#SBATCH --export=NONE 
#SBATCH --time=08:00:00 # estimated run time

source /etc/profile.d/modules.sh
module use -a /lrz/sys/share/modules/extfiles

module load cellranger/3.1.0

cellranger mkfastq --id=tiny-bcl --run=DIR/cellranger-tiny-bcl-1.2.0 --csv=DIR/cellranger-tiny-bcl-simple-1.2.0.csv

Run the job:

$ sbatch job_mkfastq.sh