[Bioperl-l] from SimpleAlign to SAM/BAM

[Jun Yin]

Hi, Albert,

Check this page for the BioPerl wrapper on next-gen sequencing results
http://bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA

And, I don't think Bio::SimpleAlign works on assembly files. It is targeted
at global alignment, e.g. clustalw output file.

Cheers,
Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Albert Vilella
Sent: Wednesday, May 19, 2010 9:36 AM
To: bioperl-l at bioperl.org
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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