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:
| 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 |
| 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.
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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.
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