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? BR, Leonor

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#___HighThrough putSequencing 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 > > _______________________________________________ > 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

No matter which package you use, you got to be aware that many junction reads are reported multiple times by TopHat if you ran TopHat with the default setting. W On May 22, 2012, at 6:31 PM, 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? > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}