On 09/16/2011 02:11 PM, Michael Lawrence wrote:
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.
Hi Rene
the 'which' argument to readGappedAlignments (it'll become 'param' with
the next release, and be a ScanBamParam object) allows you to select
regions to process, e.g., chromosome-at-a-time, to help with file size.
Martin
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
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