what is thread?

[xy6699]

Hi,

I'm an absolutely beginner in tophat. There is an option in tophat, saying --num-threads. The explanation for this is "use this many threads to align reads. The default is 1". But what does "thread" mean here? How shall I set the value of it?

Many thanks

[adaptivegenome]

number of processes to spawn on your CPU during the the alignment process

[westerman]

In general you will want to spawn no more than 1 thread per core that you have in your system. Thus if you have dual-core machine then use 2 threads. If you have a 24-core machine then use 24 threads.