[R] ShortRead with BWA

[Abhishek Pratap]

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-sequencing

best,
-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.
>
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