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My computer has dual hard drives, one SSD and one traditional spinning HDD. Will keeping any of the files used in Bowtie or Tophat alignments on the SSD instead of the HDD speed up the process? Eg. The index files, input sequence reads, output files, or (in the case of Tophat) temp files. Other specs are i7-2720QM (2.2-3.3GHz), 16GB RAM. I'm thinking the bottleneck is probably the CPU since the threads almost always run at nearly 100% but thought I would ask.
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Last edited by biznatch; 11-16-2011, 09:33 PM. -
An SSD won't help for this type of analysis. Bowtie maps the genome indices into memory, so once it's loaded the only activity from the disk should be writing out results files.
As you've seen the limitation is CPU. Bowtie allows you to spread your CPU load over many cores using the -p parameter and performance increases linearly with number of CPUs up to at least 8 cores in our tests. Tophat can also take advantage of this, but some parts of the code (calculating putative splice sites) are not multi-threaded, so will only use a single CPU. -
Thanks for the reply, I figured as much. I use 6-8 cores depending on if I need the computer for anything else while the alignments are running.Comment
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