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.para...@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]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
