[BioC] help with mapping statistics summary

Martin Morgan mtmorgan at fhcrc.org
Tue May 22 18:22:47 CEST 2012

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


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.


> BR,
> Leonor
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

More information about the Bioconductor mailing list