Hi there,
I know this issue has been already touched, perhaps several times, but
the solutions I found in the list (i.e. param=ScanBamParam(which=<...>)
doesn't seem to work.
(https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2010-December/001755.html)
I have bam files from Human Exomes, about 45 millions reads.
I imported RefSeq exons as genomic ranges using the import function of
rtracklayer from the bed file.
This is my command and the error I get
> load("refseq.exon.fixed.RData")
> UCLG_20_1<-scanBam("UCLG_20_1.fq.novo.rmdup.bam_sorted.bam",
param=ScanBamParam(which=refseq.exon.fixed))
Error: cannot allocate vector of size 156 Kb
Execution halted
My R version is
R version 2.11.1 (2010-05-31)
running on linux machines within a cluster environment.
Any idea? being it in a cluster it becomes a bit difficult to tweak
memory settings..
cheers,
Francesco
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