Thread: Tophat Run time
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Old 06-21-2010, 09:48 AM   #4
john_mu
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Location: Stanford, CA

Join Date: May 2010
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Did you run TopHat with multiple threads?

If you are running it with only one thread 17Gb of reads will take several days to run...

What is your read length? Long reads also take much longer than short ones (for the same amount of data).

Running TopHat and Maq at the same time should not cause much problems (Unless you ran TopHat with 8 threads)

Regarding your system configuration, 64Gb should be plenty of RAM for your amount of data.
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