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Thread | Thread Starter | Forum | Replies | Last Post |
High performance computing & Tophat & Cufflinks | paolo.kunder | Bioinformatics | 1 | 01-24-2012 09:02 AM |
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Advice for setting up a cpu cluster | Kennels | General | 4 | 10-14-2011 01:43 AM |
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newbler cpu core usage | malatorr | 454 Pyrosequencing | 2 | 01-12-2010 05:59 AM |
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#1 |
Member
Location: Moon Join Date: Apr 2011
Posts: 60
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We have got a huge amount of RNAseq data and we would like to optimize/maximize the performance of our computer (wisely use the computer resources to speed up assembly step).
Any suggestions for this? I know there is -p/num-threads for Tophat, how to use it and what is your suggestion for our CPU and memory? 2 X 2.93 GHz 6-Core Intel Xeon 24GB 1333MHz DDR3 Thanks a lot! |
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#2 |
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Location: Moon Join Date: Apr 2011
Posts: 60
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some people said 1 thread per core, so I should set up -p 6? Thanks!
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#3 |
Senior Member
Location: Australia Join Date: Sep 2008
Posts: 136
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Don't you have 2x6 cores so 12 cores in total? Anyway a lot of the steps in TopHat aren't multithreaded so you definitely won't get a linear speedup with more threads.
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#4 |
Member
Location: Moon Join Date: Apr 2011
Posts: 60
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Thanks!
Yeah, 12 cores, so can set up 12 threads; and the data set is too big and really need cut off the time of assembly; btw, which steps do you know are multipl-treaded? i saw some people said Bowtie and other people said adjunction parts? |
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