[Bioc-sig-seq] novoalign format support

[Wu, Xiwei]

Thanks, Martin.

The data format is available at
http://novocraft.com/downloads/download.php?filename=Linux/V2.0/NovoCraf
tV2.05.pdf

It starts at bottom of pg. 17. 

Yes, it does output SAM format, but it has two custom tags for SAM
format output. Not sure how compatible they are with Rsamtools.
Otherwise, it should be fine to wait for Rsamtools to come out.

Xiwei

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Tuesday, March 09, 2010 1:20 PM
To: Wu, Xiwei
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] novoalign format support

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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