[Bioperl-l] Getting read position information from an ACE file?

[Mark A. Jensen]

Dan -- I don't know much about Assembly, so can't help there. But can I  
encourage you and perhaps one or two others (steganographic content: fangly) 
to create a HOWTO stub out of this? Would be excellent-
cheers MAJ
----- Original Message ----- 
From: "Dan Bolser" <dan.bolser at gmail.com>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Friday, September 18, 2009 10:55 AM
Subject: [Bioperl-l] Getting read position information from an ACE file?


> Dear Perl Monkeys,
> 
> I wrote a little demo script for Bio::Assembly::IO here:
> 
> http://www.bioperl.org/wiki/Module:Bio::Assembly::IO
> 
> 
> I would very much appreciate comments, criticisms and corrections on
> that script (please just edit the wiki). For a newbie its always the
> same question, am I doing it right?
> 
> In particular, I read about the 4 possible coordinates of a read in an
> assembly. My script only retrieves two (?) of the possible four. How
> should it be adjusted to print all four coordinates for each read?
> 
> Additionally, I'm not sure how to distinguish between the trimmed read
> vs. the full length read and/or the aligned portion of the read vs.
> the full length read.
> 
> What I *really* want is the coordinates of the aligned portion of the
> read in gapped read and gapped consensus space, along with the quality
> trimmed range of the read.
> 
> The ACE file in question is produced by the gsMapper program, which is
> part of Newbler from Roche (454), so it has some small
> 'peculiarities', but I don't think they are critical for the task at
> hand.
> 
> 
> Thanks very much for any hep you can provide on any of the above issues.
> 
> Sincerely,
> Dan.
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