(1) I know that the number of threads specified (-p option) should not be larger than the number of cores available in the system. But I am wondering if there is any fixed limit on the number of threads in running Tophat regardless how many cores are available?
In other words, if the number of threads reaches certain high number, would it possibly cause segmentation fault or not speed up the process in any way?
(2) We have 24 cores in our system. I’m not sure if using 20 threads (-p 20) to run Tophat is safe and effective? What about using 24 threads (-p 24)?
(3) Since we have many large samples to run, I’m trying to figure out a good way to parallel process them.
Between these two choices: (a) running single Tophat with “-p 20” sequentially (b) running two Tophat with “-p 10” simultaneously, which choice takes less time for the same amount of samples?
Would choice (b) be faster since Tophat has some steps which do not use multithreading (but I pre-built the transcriptome index)?
On the other hand, would choice (b) use doubled memory than choice (a) which may possibly slow down the process?
Any advice would be greatly appreciated.
Thank you very much!