[Bioperl-l] from SimpleAlign to SAM/BAM

[Mark A. Jensen]

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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