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Tuesday, September 17, 2013

Tophat run time

It took me 45 hrs to map a 24G single-end RNA-seq data to human hg19 with the gtf file from GENECODE! 

I run tophat on a cluster with 1 node, 8 processors with 3gb ram for each processor (the max free resource as a regular user). I have six such files...it will take me 12 days to finish the mapping....wish I had better access to the computing resource...

a quick google confirmed that it does take that long...
http://seqanswers.com/forums/showthread.php?t=5148
"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."

2 comments:

  1. some other people's experience with tophat
    "20.8G bases (104M reads, Pair End) 1 node (16 cores) AMD 2.4GHz 96G ram
    - 28 hours
    Tophat 2 runs best with 16 cores ( single node) according to our tests otherwise it takes longer.
    STAR runs much faster ( less than 40 minutes) but needs a lot more memory (64 cores 128G ram)."

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