[BioC] how to deal with Fastq file more than 30G

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Oct 10 02:34:41 CEST 2011


On Wed, Oct 5, 2011 at 3:45 PM, wang peter <wng.peter at gmail.com> wrote:
> ---------- Forwarded message ----------
> From: wang peter <wng.peter at gmail.com>
> Date: Wed, Oct 5, 2011 at 3:44 PM
> Subject: how to deal with Fastq file more than 30G
> To: bioc-sig-sequencing at r-project.org
> IT is too slow to read them in the memory.
> who can tell me if i need split them by other program or
> call some R function to split them

In the *nix universe, you'll find a command line program
coincidentally named "split" that can do this for you.

Another option is to reconsider whether or not you really need to load
all of your reads into memory to do whatever it is that you are doing
-- if I were a gambling man, I'd put money on "no" ...


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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