[BioC] any package to do gene expression value estimation

[Martin Morgan]

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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