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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Kind request for suggestions from those experienced with large data #2012

Closed saeedfc closed 5 years ago

saeedfc commented 5 years ago

Any updates on this? I'm getting the same issue with ~400K cells across 30 datasets. Should I just switch to RPCA for now?

(300 GB of RAM....will try again with 1TB)"

Originally posted by @davemcg in https://github.com/satijalab/seurat/issues/1720#issuecomment-516948860

Sorry for a silly question here. So far I have only worked with a normal workstation for upto 8k cells. Soon we are planning big experiments with 15-20 samples of 10k cells each (150k - 200k cells) (~18000 features) Is 128GB RAM sufficient for the pipeline (SCT & Integration included). But seeing this thread @davemcg using 300GB RAM and still not able to work with 400k cell, I am not sure about what to buy.

satijalab commented 5 years ago

We cannot advise on hardware, but if you read the rest of that thread, we provide an alternative approach for running extremely large datasets even in the absence of a high-memory machine