[Bioperl-l] from SimpleAlign to SAM/BAM

[Albert Vilella]

Awesome, thanks. I'll give it a try :-)

On Wed, May 19, 2010 at 2:34 PM, 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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>>
>>
>
>