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Re^2: Deconvolutinng FastQ files

by BrowserUk (Patriarch)
on Aug 06, 2012 at 19:57 UTC ( [id://985818]=note: print w/replies, xml ) Need Help??


in reply to Re: Deconvolutinng FastQ files
in thread Deconvolutinng FastQ files

I hate to be there bearer of bad tidings here, but if you'd ever tried using Tie::File on a 34GB file, you'd never be suggesting it to others. It would take weeks to complete.


With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

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Re^3: Deconvolutinng FastQ files
by Kenosis (Priest) on Aug 06, 2012 at 21:15 UTC

    Oh, this is sad. I just had the script work on a 1G+ file, and extrapolated the time to about 17hrs of processing for a 34G file. It's not weeks, but it's also not practical. Didn't realize that Tie:File was so inefficient with large files.

    Good call to point this out, BrowserUK! Will place an "Update:" in the posting.

      :D Thank you for the help. Although, it will probably take me a while to understand what you guys are talking about.

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