[Bioperl-l] from SimpleAlign to SAM/BAM

[Mark A. Jensen]

B:T:R:Samtools wraps Bio::Samtools
  ----- Original Message ----- 
  From: Lincoln Stein 
  To: Mark A. Jensen 
  Cc: Albert Vilella ; bioperl-l at bioperl.org 
  Sent: Wednesday, May 19, 2010 12:40 PM
  Subject: Re: [Bioperl-l] from SimpleAlign to SAM/BAM


  Bio::Samtools, which is separate from bioperl but compatible with it, provides read/write access to SAM and BAM via Heng's C library.


  Lincoln


  On Wed, May 19, 2010 at 9:34 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

    Albert-- have a look at Bio::Tools::Run::Samtools which incorporates the use of Bio::Assembly::IO::sam (I think). I know there is only read capability for B:A:I:sam, but Samtools may give you the appropriate wrapper for doing writes (some assembly (so to speak) required...)-- cheers MAJ
    ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>

    To: <bioperl-l at bioperl.org>

    Sent: Wednesday, May 19, 2010 4:36 AM

    Subject: [Bioperl-l] from SimpleAlign to SAM/BAM



      Hi,

      I would like to know what would be the best way to generate a SAM/BAM file
      with cDNA alignments against the human reference from a bunch of
      Bio::SimpleAlign
      cDNA multiple sequence alignment objects.

      Considering I've got a way to map the cDNAs to chromosome coordinates,
      how can I generate a SAM/BAM file with ~1,000,000 entries against ~23.000 human
      coordinates?

      As far as I can see, there is an Bio::Assembly::IO::sam.pm which loads
      assemblies.
      Should I be using some other tool existing not in bioperl?

      Cheers,

      Albert.
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  -- 
  Lincoln D. Stein
  Director, Informatics and Biocomputing Platform
  Ontario Institute for Cancer Research
  101 College St., Suite 800
  Toronto, ON, Canada M5G0A3
  416 673-8514
  Assistant: Renata Musa <Renata.Musa at oicr.on.ca>