[BioC] help with mapping statistics summary

[Martin Morgan]

On 05/22/2012 01:31 AM, Leonor Carvalho wrote:
> Hi,
>
> I am pretty new using the bioconductor and I have some RNAseq data on which I
> had performed and TopHat and I need to perform a mapping summary statistics
> from the results. I have a pretty large BAM file of accepted hits (aprox.
> 17GB).
>
> I´ve been looking at the bioconductor packages and I found the Rsamtools, that I
> think maybe I can used to this propose, but can anyone give me any suggestion
> of some other package or how could I do this statistics summary?

EDASeq from this page

http://bioconductor.org/packages/release/BiocViews.html#___HighThroughputSequencing

including its vignette might provide some inspiration, perhaps in 
conjunction with Rsamtools::scanBam or 
Rsamtools::readBamGappedAlignments. Use 
ScanBamParam(which=GRanges(<...>)) to read in part of a file if memory 
is an issue.

Martin

>
> BR,
>
> Leonor
>
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