[BioC] about reduce function in GenomicRanges

[Steve Lianoglou]

Hi,

On Tue, Jan 17, 2012 at 7:42 PM, Tarca, Adi <atarca at med.wayne.edu> wrote:
> Hi Michael,
>
> Thanks for the advice. Briefly, this is the code that I have so far for dealing with paired end Illumina data. It runs ok on a chunk of the alignment object, but on an entire thing it is taking too much memory. A 32GB Ram 64 bit machine can't do it:
>
> aln <- readGappedAlignments(filePath,use.names=TRUE)
> strand(aln) <- "*"
> aln=as(aln,"GRangesList")
> nms=names(aln)
> names(aln)<-NULL
> aln=unlist(aln)
> aln=split(aln,nms)
> aln=range(aln)
>
> The last line is the limiting step.
> Any suggestion how to decrease the memory consumption here?

Out of curiosity:
* how big is your bam file?
* are your running on windows? I think there's some tom-foolery you
need to do to tweak windows memory usage. If your on *nix, then that's
not the problem

For the time being, I'd suggest just reading in the reads one
chromosome at a time and calculating the range over each independently
...

HTH,
-steve

-- 
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