Running 10x Cell Ranger Pipeline
Notebook: 09-25-2025
Cynthia S. Cardinault
Modes to Run Cell Ranger
Running Cell Ranger isn’t a one-size-fits-all process. Depending on your setup, you can choose between different modes each with its own flavor, a bit like deciding whether to cook at home, order takeout, or head to a cafeteria.
So, depending on your setup, you have a few options:
Local or Institutional HPC
Most researchers run Cell Ranger on an institutional High-Performance Computing (HPC) cluster or a dedicated Linux server. A typical run may need 64 GB RAM or more plus multiple CPU cores. So if your lab has access to an HPC, that’s often the easiest path.
Genomics Cloud Analysis
Don’t have a big server? No problem. The 10x Genomics Cloud Analysis platform is available almost everywhere (except China, Hong Kong, and embargoed countries). Good news Mexico and most of Latin America are included.
- Free tier: Up to 50 analyses per month—perfect for starting out.
- Extras: You can transfer projects between accounts, and collaborative features are on the way.
- Caveat: Paid upgrades are mostly limited to the U.S. and Canada.
General Cloud Platforms
If you prefer flexibility, you can spin up a virtual machine on AWS, Google Cloud, or another provider. Just pick a high-memory instance, install Cell Ranger, upload your FASTQs, and pay only for what you use. This is a great option if you need scalability on demand.
Alternatives to Cell Ranger
While Cell Ranger is the gold standard, you might explore community tools too:
- STARsolo – efficient and highly comparable to Cell Ranger.
- kallisto/bustools (Alevin-fry) – much faster and lighter on memory.
Wrapping Up
Cell Ranger may look intimidating at first, but once you run it a couple of times you’ll realize it’s a solid, reliable backbone for single-cell data processing. Whether you use an HPC, the free cloud tier, or your own server, it’s the first step in turning sequencing reads into biological insights.
My advice? Start with the simplest setup you have access to (often your institution’s HPC or the 10x Cloud free tier), then scale up once your projects get bigger.
Benchmarking Run Modes
Curious how they stack up?
Hope you have a find useful alternatives to run your pipeline. Dont’t miss my next notes talking about Secondary Analysis Alternatives
References
Disclaimer: Some image(s) were generated by a large language model based on a user-provided concept and is intended for illustrative and educational purposes only.