[Bioperl-l] from SimpleAlign to SAM/BAM

[Albert Vilella]

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.