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:[email protected]] Sent: Tuesday, March 09, 2010 1:20 PM To: Wu, Xiwei Cc: [email protected] 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 > > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}} > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
