BinAC/Software/Cellranger
|
The main documentation is available on the cluster via |
| Description | Content |
|---|---|
| module load | bio/cellranger |
| License | Cell Ranger License |
| Citing | How to cite Cell Ranger |
| Links | Cell Ranger Homepage | 10x Genomics Homepage | Command Line Arguments |
| Graphical Interface | No |
Description
Cell Ranger is a set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from 10x Genomics Chromium Single Cell data.
Cell Ranger Versions
Check available Cell Ranger versions:
module avail bio/cellranger
Usage
Loading the module
Load a specific Cell Ranger version:
module load bio/cellranger/9.0.1
Telemetry
Starting with Cell Ranger v9.0, anonymized telemetry data is collected and sent to 10x Genomics. We already disabled sending telemetry data in the module via:
TENX_DISABLE_TELEMETRY=1
Cell Ranger References
References for Cell Ranger 9.0.1 are located at /pfs/10/project/db/cellranger/2024-A.
Upon loading the module, the variable CELLRANGER_REFERENCES points to this location and can be used in SLURM job scripts.