[BioC] fastq upload time

Alex Gutteridge alexg at ruggedtextile.com
Wed Sep 22 14:21:44 CEST 2010


On Wed, 22 Sep 2010 08:12:27 -0400, Sean Davis <sdavis2 at mail.nih.gov>
wrote:
> On Wed, Sep 22, 2010 at 8:07 AM, <Daniel.Berner at unibas.ch> wrote:
> 
>> Hi there
>> I have a solexa fastq file containing some 27 million reads (file size
>> approx. 4 GB). my plan is to upload this into R for subsequent editing
>> with
>> ShortRead tools. The R version is 64-bit linux, the computer has 8 GB
>> RAM.
>> Can anybody provide a rough estimate of how long the input will take?
>> hours,
>> days...?
>>
> 
> Depending on disk and network speeds, perhaps a few minutes.  8GB is
pretty
> small, though.  You'll have to give it a try to see if it all fits into
> memory.
> 
> Sean

Yes, my experience with ShortRead and files this size was that 8GB was not
enough. If it is compatible with your planned analysis I would split the
file according to chromosome and work from those.

-- 
Alex Gutteridge



More information about the Bioconductor mailing list