It sounds like you're trying to use BED as an alternative to BAM? Probably
not a good idea, especially at this scale. Why are you aiming for a
GenomeData? A GappedAlignments might be more appropriate. See
GenomicRanges::readGappedAlignments() for bringing a BAM into a
GappedAlignments.

This page might help:
http://bioconductor.org/help/workflows/high-throughput-sequencing/#sequencing-resources

But it could really be improved.

Michael

On Fri, Sep 16, 2011 at 1:44 PM, Rene Paradis <rene.paradis@genome.ulaval.ca
> wrote:

> Hello,
>
> I am experiencing a problem regarding the load in memory of bed files of
> 30 GB. my function read.table unleash the error : Error in unique(x) :
> length xxxxxx is too large for hashing.
>
> this is generated by the function MKsetup of the unique.c file. Even by
> increasing by 10 000x the value, the error persists. I believe the
> function pushes more data in ram, but I am not sure this is the good way
> to focus on.
>
> Ultimately, I would like to produce a GenomeData object from either a
> BAM file or a bed file.
>
> has someone ever worked with very very big BAM files (about 30 GB)
>
> thanks
>
> Rene paradis
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

