[Bioc-sig-seq] novoalign format support

[Martin Morgan]

On 03/08/2010 01:59 PM, Wu, Xiwei wrote:
> Hi, all,
> 
> Is there any plan to support Novoalign format in readAligned function in
> the ShortRead package? We have been using it as a standard tool, given
> its alignment accuracy, but we have to convert it to MAQ format to use
> with readAligned function so far. 

I couldn't easily find a description of their data format.

> Also, when Rsamtools will become available in the development version of
> R? 

The intention is that Rsamtools will be in the next Bioconductor
release, which is now not that far away (a couple of months). I notice
that novoalign says that they are able to export SAM files so maybe
there is not a big need for importing their format directly?

Martin

> Xiwei Wu, Ph.D.
> Associate Director, Bioinformatics Core
> Assistant Research Professor
> Department of Molecular Medicine
> Beckman Research Institute
> City of Hope
> 
> 
> 
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Martin Morgan
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