Cell Ranger ATAC, printed on 05/31/2020
Cell Ranger ATAC pipelines run on Linux systems that meet these minimum requirements:
See the 10x Genomics OS Support page for further information.
In order to run in cluster mode, the cluster needs to meet these additional minimum requirements:
In order to run cellranger-atac mkfastq, the following software needs to be installed:
|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|
|The following plots are based on time trials using Amazon EC2 instances, our PBMC_5k dataset, and version 1.1 of Cell Ranger ATAC. These plots will not be updated with every subsequent release of Cell Ranger ATAC, unless pipeline performance changes significantly.|
Here is cellranger-atac count walltime as a function of available memory. In general, you can improve performance by allocating more than the minimum 64GB of memory to the pipeline. There is notable diminishing return beyond 128GB.
Here's cellranger-atac count walltime as a function of threads. If your system has ≫32 logical cores, you may want to run with --localcores=32 since there is diminishing return beyond 32 threads.