[BioC] help with mapping statistics summary
mtmorgan at fhcrc.org
Tue May 22 18:22:47 CEST 2012
On 05/22/2012 01:31 AM, Leonor Carvalho wrote:
> 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.
> 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
including its vignette might provide some inspiration, perhaps in
conjunction with Rsamtools::scanBam or
ScanBamParam(which=GRanges(<...>)) to read in part of a file if memory
is an issue.
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