[Biojava-l] Saving back chromatogram?

[Andy Yates]

As far as I'm aware no there shouldn't be a problem with this solution.

However have you investigated any other mechanisms for doing this kind
of contig editing/assembly work? I know that people at the Sanger Centre
use a program called gap4 which has powered just about every assembly
they have done. It's available from:

http://www.sanger.ac.uk/Software/production/staden/ (bit of info here)

http://staden.sourceforge.net/staden_home.html

Have a look at it as I feel that this is exactly what you are attempting
to do.

Andy

Ashika Umanga Umagiliya wrote:
> Cheers.
> 
> 
> I still haven't implemented the editor.I assume for basecall editing, I
> can use 'Edit' class.
> 
> Like:
> 
> ABIFChromatogram a;
> ..
> ..
> a.getBaseCalls().edit(new Edit(.......))
> 
> 
> And for Quality values, I am hoping to read and store Qualitly files
> generated by 'phred'.And when user edit the basecall, I am planing to
> edit stored quality values accordinly.
> Finally the fasta file is generated using
> ABIFChromatogram.getBaseCalls()...
> and Quality file will be generated using the structure I used above.
> 
> Any issues with this approach?
> 
> Many thanks,
> Umanga
> 
> 
> Russ Kepler wrote:
>> On Thursday 19 February 2009 22:48:45 Ashika Umanga Umagiliya wrote:
>>
>>  
>>> My problem is can I use the same Quality files ,with  the modified
>>> callbases ?
>>>     
>>
>> Edit the quality data in parallel with the chromatogram.  I would
>> assume that the editor is relatively sure of their edits, so I would
>> give them a high confidence level when I generate the trace fasta and
>> quality file.
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