multithreading is not working for apply_DEXSeq_test_seurat module about sierra

[rj-patrick]

Hi @AidenSb,

It could be a memory issue - are you able to run the function on a subset of the data and/or a smaller numbers of cores?

Also, depending on the size of your dataset, the multithreading functionality that gets passed to DEXSeq may not be beneficial. I've found at least for a standard scRNA-seq experiment size (few thousand to few 10s of thousand cells) using multithreading doesn't seem to outweigh the cost of setting up the workers. In the case of running hundreds of tests it could be better to wrap a parallel function around the call to the DU functions.

Hope that's helpful.

Cheers,
Ralph

[AidenSb]

Hi Ralph thanks for the reply. Yes, indeed I ended up making a parallel function to run. Thanks