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
Example:
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.
#!/bin/bash #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