[BioC] any package to do gene expression value estimation
Martin Morgan
mtmorgan at fhcrc.org
Tue Oct 25 16:46:46 CEST 2011
On 10/25/2011 07:43 AM, wang peter wrote:
> thank u:
> so the best methods is
> use bwa/bowtie to get the sam file
> then use R package to anaylize sam file and get the information which
> you want.
> but, how to deal with huge sam files?
> do i need writing a perl scripts to split the sam file and process them
> by R.
> then combine them?
> any other good ways?
use Rsamtools package. Make your aligner produce BAM files, or use
Rsamtools::asBam to convert sam to bam; bam files are faster to load /
more flexible. For many purposes GenomicRanges::readGappedAlignments is
sufficient; Rsamtools::scanBam for maximum flexibility.
Martin
> shangao
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