[R] ShortRead with BWA

[mtmorgan at fhcrc.org]

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.
>
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