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Old 05-16-2010, 07:04 PM   #1
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Default TopHat approximate run time & memory usage?

Hi everyone,

I'm using TopHat to map my RNA-seq reads to splice junctions for use in Cufflinks, but it's been taking a bit longer than I expected. One sample I ran (as an initial test) has been going for ~34 hours, and the tophat_out folder is using up around 76 GB of space. By looking in the logs, it seems to be on the "segment_juncs" step.

Each of the individual samples I hope to align have roughly 90 million reads (@ 50 nt) over 3 lanes, and I'm aligning to the human genome (hg19).

Would anyone know how long I should expect the program to run for, and also how much disk space it'll need per sample?


edit: I'm using single-end reads

Last edited by xinchen; 05-16-2010 at 07:06 PM.
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Old 05-16-2010, 07:20 PM   #2
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It routinely takes ~40 hours for me (~45 million reads, with - p 4 to use four threads and 16G RAM). It will delete the huge temp files it generates, so the disk usage may not be that much of any issue.
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Old 05-16-2010, 11:23 PM   #3
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I'm not sure but i think that TopHat need for 75million reads about 3 Days...
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Old 05-17-2010, 01:03 PM   #4
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Thanks! It ended up taking ~50 hours for my test sample, which isn't too long
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Old 05-18-2010, 02:47 AM   #5
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How can you guys compare run time and memory usage without stating the CPU and RAM you are using???
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