Hi Duke While your mails are most welcome to this mailing list. You may find the following mailing list more useful as it caters to the Bioconductor and Next Generation Sequencing stuff.
Bioc-sig-sequencing mailing list > bioc-sig-sequenc...@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing best, -Abhi On Tue, Apr 27, 2010 at 6:07 PM, Duke <duke.li...@gmx.com> wrote: > Dear folks, > > Please welcome a newbie both to R and the mailing list :). I am currently > working on a sequencing project, and heard about R as well as some of its > packages for next gen sequencing, and decided to give it a try. Starting > with ShortRead, I found a document > (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) > which does mention that readAligned was extended to support SAM format (for > example, BWA output). > > So I tried readAligned with > > BWAAln <- readAligned(BWAFile, type = "BWA") > > but then I got error: > >> BWAAln <- readAligned(BWAFile, type = "BWA") > Error: UserArgumentMismatch > arugment 'type' had value 'BWA' allowable values: 'SolexaExport' > 'SolexaAlign' 'SolexaPrealign' 'SolexaRealign' 'SolexaResult' > 'MAQMap' 'MAQMapShort' 'MAQMapview' 'Bowtie' 'SOAP' > > It looks like ShortRead does not support BWA. Am I right, or what am I doing > wrong? Anybody has any idea? > > Thanks, > > D. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.