Single Cell Gene Expression
Cell Ranger , printed on 03/22/2019
Cell Ranger pipelines run on Linux systems that meet these minimum requirements:
- 8-core Intel or AMD processor (16 cores recommended)
- 64GB RAM (128GB recommended)
- 1TB free disk space
- 64-bit CentOS/RedHat 6.0 or Ubuntu 12.04
- The minimum requirement of 64GB RAM will allow cellranger aggr to aggregate up to 250k cells, more memory will be required beyond that.
The pipelines also run on clusters that meet these additional minimum requirements:
- 8-core Intel or AMD processor per node
- 6GB RAM per core
- Shared filesystem (e.g. NFS)
- SGE or LSF batch scheduling system
Most software dependencies come bundled in the Cell Ranger package. However,
cellranger mkfastq also requires:
- Illumina bcl2fastq. Version 2.17 or higher is preferred and supports most sequencers running RTA version 1.18.54 or higher. If you are using a NovaSeq, please use version 2.20 or higher. If your sequencer is running an older version of RTA, then bcl2fastq 1.8.4 is required by Illumina.
- Cell Ranger runs locally by default (or when specified as --jobmode=local), using 90% of available memory and all of the available cores. To restrict resource usage, please use the --localmem and --localcores options (see cellranger count --help).
- Many Linux systems have default user limits (ulimits) for maximum open files and maximum user processes as low as 1024 or 4096. Because Cell Ranger spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. We recommend higher limits:
user open files
system max files
10k per GB RAM available to Cell Ranger
64 per core available to Cell Ranger