[Bioperl-l] from SimpleAlign to SAM/BAM

[Lincoln Stein]

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.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
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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>