Hi Duke --

Quoting Duke <duke.li...@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.

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