[R] ShortRead with BWA

[Duke]

On 4/27/10 6:29 PM, mtmorgan at fhcrc.org wrote:
> 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
>

Great resources, thanks Abhi and Martin. And yes you are right, I have 
an old version of R on my Mac Pro. I am installing the newest now :).

Thanks,

D.