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Using 10x Genomics Cell Ranger

OAsis cluster has Cell Ranger pre-installed. Users may load it from Lmod. The following is an example of converting a tiny sample from BCL format to FASTQ using Cell Ranger with a single node and multinode (cluster mode). 

First of all, we will download the sample file we need:

# set up our working directory
mkdir -p ~/mrotest
cd ~/mrotest

# download and extract the sample files from 10xgenomics
wget https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz
wget https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv
tar -zxvf cellranger-tiny-bcl-1.2.0.tar.gz
rm cellranger-tiny-bcl-1.2.0.tar.gz
tree -L 2 cellranger-tiny-bcl-1.2.0/

Now, we are ready to convert the sample to the FASTQ format.

Local mode (single node, run interactively for testing purposes)

# request a node, and run Cell Ranger interactively (suitable for troubleshooting issues)
srun -p batch -c16 --mem 128G --pty bash

# inside the shell, load the respective modules
module load GCC/11.3.0 bcl2fastq2 CellRanger

# run the case
rm -rf test
cellranger mkfastq --id=test \
  --run=./cellranger-tiny-bcl-1.2.0 \
  --csv=./cellranger-tiny-bcl-simple-1.2.0.csv

# result will be located in the test folder in the current directory

Local mode (single node, scheduled)

For a practical but relatively small case, you can run Cell Ranger in local mode. Following is an example job script, you may name it run.sh.

#!/usr/bin/env bash

#SBATCH -J mkfastq
#SBATCH -o mkfastq.out
#SBATCH -e mkfastq.out
#SBATCH -p batch
#SBATCH -n 1 -c 16
#SBATCH --mem-per-cpu=8G

module load GCC/11.3.0 bcl2fastq2 CellRanger

rm -rf test

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

Then you can submit the job by running: sbatch run.sh

Cluster mode (multinode)

Multiple nodes may be needed for large cases. First, we have to set up a job script template. Cell Ranger will then submit jobs leveraging the template. Set up a new file called slurm.template as follows.

#!/bin/bash
#SBATCH -p batch
#SBATCH -J __MRO_JOB_NAME__
#SBATCH -o __MRO_STDOUT__
#SBATCH -e __MRO_STDERR__
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c __MRO_THREADS__
#SBATCH --mem=__MRO_MEM_GB__G
#SBATCH --export=ALL
#SBATCH --signal=2
#SBATCH --time=8:00:00

 __MRO_CMD__

Then you may launch Cell Ranger in cluster mode.

module load GCC/11.3.0 bcl2fastq2 CellRanger

cellranger mkfastq --id=test \
  --run=./cellranger-tiny-bcl-1.2.0 \
  --csv=./cellranger-tiny-bcl-simple-1.2.0.csv \
  --jobmode=slurm.template \
  --maxjobs=3 --jobinterval=1000 --mempercore=4

# Here, we restrict Cell Ranger to launch at most 3 concurrent jobs.
# A 1-second interval will be waited between each job.
# 4 GB of memory is requested per core.
# You may play around with these parameters based on your need.

Reference links:
https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-fq
https://www.10xgenomics.com/support/software/cell-ranger/latest/advanced/cr-cluster-mode

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