Search
Question: ShortRead with BAM
0
gravatar for Duke
7.6 years ago by
Duke210
Duke210 wrote:
Hi all, I am totally new to both R and BioConductor, so please be easy on me. I just updated my R package to 2.11, and installed new ShortRead package, but it seems that I am doing something wrong, and that there is some changes from ShortRead 1.5 to 1.6 (like the command format etc...). I tried to read a BAM file by creating a file as follow: library(ShortRead) sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs') ap <- analysisPath(sp) (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM")) but running the above just gave me the content of dirPath function. My package infos is: > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 [4] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 loaded via a namespace (and not attached): [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0 Anybody has any idea? Thanks, D.
ADD COMMENTlink modified 7.6 years ago by James W. MacDonald45k • written 7.6 years ago by Duke210
0
gravatar for James W. MacDonald
7.6 years ago by
United States
James W. MacDonald45k wrote:
Hi Duke, Still the wrong list. You want Bioc-sig-sequencing. Duke wrote: > Hi all, > > I am totally new to both R and BioConductor, so please be easy on me. I > just updated my R package to 2.11, and installed new ShortRead package, > but it seems that I am doing something wrong, and that there is some > changes from ShortRead 1.5 to 1.6 (like the command format etc...). I > tried to read a BAM file by creating a file as follow: You don't want the ShortRead package. You want Rsamtools, and the scanBam() function. See ?scanBam for more info. Best, Jim > > library(ShortRead) > sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs') > ap <- analysisPath(sp) > (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM")) > > but running the above just gave me the content of dirPath function. My > package infos is: > > > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 > [4] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0 > > Anybody has any idea? > > Thanks, > > D. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 7.6 years ago by James W. MacDonald45k
On 4/28/10 10:17 AM, James W. MacDonald wrote: > Hi Duke, > > Still the wrong list. You want Bioc-sig-sequencing. Thanks :D. I thought ShortRead (and other NGS packages) is in BioConductor group too, but I forgot cc'ing to bioc-sig-sequencing group. > > Duke wrote: >> Hi all, >> >> I am totally new to both R and BioConductor, so please be easy on me. >> I just updated my R package to 2.11, and installed new ShortRead >> package, but it seems that I am doing something wrong, and that there >> is some changes from ShortRead 1.5 to 1.6 (like the command format >> etc...). I tried to read a BAM file by creating a file as follow: > > You don't want the ShortRead package. You want Rsamtools, and the > scanBam() function. See ?scanBam for more info. Thanks for pointing this out. I will try Rsamtools. But readAligned does have *BAM* type now. How can I use it? D. > > Best, > > Jim > > >> >> library(ShortRead) >> sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs') >> ap <- analysisPath(sp) >> (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM")) >> >> but running the above just gave me the content of dirPath function. >> My package infos is: >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 >> [4] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0 >> >> Anybody has any idea? >> >> Thanks, >> >> D. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 7.6 years ago by Duke210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 310 users visited in the last hour