Speed up Seurat FindClusters execution?
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4 months ago
CTLong ▴ 120

Hi all,

I am processing a scRNA-seq dataset of 200k cells, and am at the stage of finding clusters with a resolution of 2. The FindClusters function from Seurat seems to take a long time to run. Wondering if anyone have any ideas how to speed up the execution, and which method is most efficient (with less tradeoff in the clustering quality). Currently, I have three alternatives in mind:

1) Decreasing the resolution from 2 to 0.8 or even lower

2) Use sparse matrix with do.sparse = TRUE (but this is no longer available in Seurat V5, is there a workaround?)

3) Process it on HPC (my computer is quite powerful (64Gb RAM) and the HPC queueing usually takes a long time if a lot of resources are demanded, also prone to error hence re-queueing).

Thanks for the help.

Seurat • 735 views
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4 months ago
fracarb8 ★ 1.7k

Unfortunately, FindClusters works in parallel (future) only when multiple resolution are passed ( I assume 1 cpu x resolution). That was true for seurat v4, and I am not sure if it is still true with seurat 5, as they remvoed that vignette

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4 weeks ago
Picasa ▴ 650

any solutions ?

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I overcame this by running it on HPC

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