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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 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...
"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."


  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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