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10x Genomics
Single Cell ATAC

System Requirements

Cell Ranger ATAC

Cell Ranger ATAC pipelines run on Linux systems that meet these minimum requirements:

See the 10x Genomics OS Support page for further information.

The pipelines also run on clusters that meet these additional minimum requirements:

Software Dependencies

Most software dependencies come bundled in the Cell Ranger ATAC package, but certain pipeline pieces may require other software. cellranger-atac mkfastq also requires Illumina® bcl2fastq. bcl2fastq must be version 2.17 or higher. It supports most sequencers running RTA version 1.18.54 or higher. If you are using NovaSeq™, the pipelines require version 2.20 or higher. If your sequencer is running an older version of RTA, then the pipelines require bcl2fastq 1.8.4.

Resource Limits

Limit Recommendation
user open files 16k
system max files 10k per GB RAM available to Cell Ranger ATAC
user processes 64 per core available to Cell Ranger ATAC