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Hello,
I have a cohort of ~500 human RNAseq samples that I want to run DEXSeq on. Running the analysis on a single machine even with multiple cores is taking prohibitively long. I want to run it on a LSF cluster and distribute the computation across multiple machines(nodes). I have gone through the documents available with DEXSeq but it's not clear to me how I can set up such an analysis. I'll be grateful for a pointer on how I can set up such an analysis on the cluster.
Thanking You,
Vakul
Hi Vakul,
You would need to create a BatchJobsParam instance with your cluster configuration, the BiocParallel vignette has some examples on how to do this. Then you could pass this instance to the BPPARAM parameter of the DEXSeq functions.
Alejandro
Hi, Alejandro,
Thanx! I'll look into the vignette and give it a shot.
Thank you for the pointer!
Vakul