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Cell Ranger

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

Cell Ranger is available as a module on Apocrita.

Usage

To run the default installed version of Cell Ranger, simply load the cellranger module:

$ module load cellranger
$ cellranger
cellranger cellranger-X.Y.Z

Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data

Usage: cellranger <COMMAND>

Commands:
  count
  multi
  multi-template
  vdj
  aggr
  reanalyze
  mkvdjref
  mkfastq
  testrun
  mat2csv
  mkref
  mkgtf
  upload
  sitecheck
  help

Options:
  -h, --help     Print help
  -V, --version  Print version

For more information regarding each analysis pipeline, pass the --help switch after the pipeline sub-command (i.e. cellranger count --help).

Local operating mode

The local mode will execute the pipeline on a single machine, usually within a cluster job. To run all executions inside a single job, this is the desired mode.

Cores and Memory Requests

To avoid overloading a node, set the --localcores ${NSLOTS} option to restrict Cell Ranger to use the specified number of cores to execute pipeline rather than all cores available.

To prevent your job from being killed by the scheduler for using more memory than requested, set the --localmem option to restrict Cell Ranger to use specified amount of memory (in GB) to execute pipeline stages rather than to use 90% of total memory available.

Example job

Serial job

Here is an example job running on 4 cores and 16GB of memory to generate single-cell gene counts for a single library, in local mode:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G

module load cellranger

cellranger count --id 1234 \
                 --transcriptome example_transcriptome \
                 --fastqs raw_data.fastq \
                 --sample 1234 \
                 --create-bam false \
                 --disable-ui \
                 --jobmode local \
                 --localcores ${NSLOTS} \
                 --localmem 4

Reference