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.
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-sequencing at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencingbest, -Abhi On Tue, Apr 27, 2010 at 6:07 PM, Duke <duke.lists at 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 at 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. >
Hi Duke -- Quoting Duke <duke.lists at gmx.com>:> 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?Welcome to R! But actually, I should be saying 'welcome to Bioconductor!' and you should be on the Bioconductor (or Bioc-sig-seq) mailing list http://bioconductor.org/docs/mailList.html because ShortRead is a Bioconductor package. BWA produces SAM files, and SAM files can be processed, using samtools, to (sorted, indexed) BAM files. And BAM files can be read in using readAligned in the just released Bioconductor 2.6 packages. It's worth getting your data into BAM files anyway, e.g., for viewing with the IGV. I mentioned 'just released', and although you didn't provide the output of sessionInfo() (basically essential for any post) I can see that, although you're a new-comer, it's time to update your R to version 2.11, and update Bioconductor to the corresponding version 2.6. You might look at http://bioconductor.org/docs/install/ While google and trial and error are one way of getting help, you might as well get the vignettes from the package you have installed browseVignettes("ShortRead") and discover the R help system help.start() library(ShortRead) help(package="ShortRead") ?readAligned It'll be more effective in the long run. Martin> Thanks, > > D. > > ______________________________________________ > R-help at 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.