biojava-l

Hi again Andy ,

Thank you for all your help , it was a matter of setting an option in  
ChromatogramGraphic


ChromatogramGraphic chromaGfx;
.
.
chromaGfx.setOption(Option.SUBPATH_LENGTH, new Integer(
                   Integer.MAX_VALUE));


Now I can see the entire trace-plot ..  Everything is just fine :)


Best Regards,
Umanga

Andy Yates wrote:
> Hi Umanga,
>
> Glad you've got it rendering though now :)
>
> My best guess is that the trace have been truncated by the generating
> program or the file writing is incomplete which I doubt due to the way
> SCF files are constructed. So my money is on Phrap/Phred doing a bit of
> quality control with the end of the trace. Why it hasn't truncated the
> base calls as well I do not know and is probably a question better
> suited to the people who write/maintain Phred & Phrap.
>
> Sorry I can't be of that much more help :(
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
> > Hi Andy ,
> >
> > Thanks for the help.I was doing all wrong !
> > Instead of using AB1 raw data , I used SCF  generated by Phrep and used
> > the offset values from ACE file.
> > Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
> >
> > But still one problem .As can be seen in the picture, at the end of the
> > graph, some part of the trace-plot is missing for last bases.
> > Any idea whats going on here ?
> >
> > Thanks in advance,
> > Umanga
> >
> > Andy Yates wrote:
> >     
> > > Hi Umanga,
> > >
> > > In terms of getting the offset I'm not sure. That information should be
> > > provided via the ACE file or from some other output from phrap; its not
> > > the responsibility of the AB1 file to contain this information. The
> > > phred output (which phrap uses under the scenes I think) which does
> > > contain this information is the SCF output but in this situation you are
> > > not rendering the processed output from the ABI sequencer. You are
> > > actually displaying:
> > >
> > > ABI Raw output -> phred basecalled/processed
> > >
> > > So if there is a reason why you want to show the ABI processed data then
> > > I'm not sure how to marry it to the phrap output. Otherwise just use the
> > > traces phrap outputs and see what happens.
> > >
> > > Andy
> > >
> > > Ashika Umanga Umagiliya wrote:
> > >  
> > >       
> > > > Hi Andy,
> > > >
> > > > Thank you for the reply.
> > > > Earlier problem was I had not applied the compliment in the
> > > > ChromatoGraph.
> > > > Now I could inspect the alignment with the Phrap calls
> > > >
> > > > Please refer :  http://i43.tinypic.com/e5iu12.png
> > > >
> > > > I have drawn orange underlines from where the two sequences matches.
> > > > But I had to hardcode x1 and x2 offset values to make the graphs align
> > > > with the Phrap basecalls.
> > > > So as for my question
> > > > http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
> > > > somehow get all (or fill) all the callbases same as in ACE , I can align
> > > > easily.
> > > >
> > > >
> > > > Best Regards,
> > > > Umanga
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Andy Yates wrote:
> > > >    
> > > >         
> > > > > Hi Ashika,
> > > > >
> > > > > AB1 files will contain a different basecall to one generated by phrap
> > > > > since (as far as my memory serves me) ABI's platform has a basecaller
> > > > > built in. This is the one which is coded into the AB1 file & therefore
> > > > > chromatogram graphic will pick up on that one. However it's very odd
> > > > > that the Phrap calls are so distant from the trace itself.
> > > > >
> > > > > I would have hoped that the ACE file would have contained some kind of
> > > > > called base -> peak position in the chromatogram. There is always the
> > > > > option of getting phred to output a SCF file which should contain this
> > > > > information & see what it thinks its doing. SCFs can be parsed by
> > > > > BioJava so you should be able to push it straight into your program &
> > > > > let it handle it.
> > > > >
> > > > > Andy
> > > > >
> > > > > Ashika Umanga Umagiliya wrote:
> > > > >  
> > > > >      
> > > > >           
> > > > > > Greetings all,
> > > > > >
> > > > > > Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
> > > > > > image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
> > > > > >
> > > > > >
> > > > > > As shown in image (1) , I draw the basecall sequences of AB1 file,by
> > > > > > parsing the ACE file generated by Phrap.That is ,for upper part I
> > > > > > do not
> > > > > > read AB1 file.Only read values from ACE file.(values under 'RD' tag in
> > > > > > ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
> > > > > > 'sampleA-S-F.AB1'.
> > > > > >
> > > > > > For the bottom part- that is to draw Chromatogram, I use Biojavas
> > > > > > 'ChromatogramGraphic' class.
> > > > > >
> > > > > > I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
> > > > > > basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
> > > > > > on...(like
> > > > > > in ChromasPro).
> > > > > >
> > > > > > But I noticed that basecall sequence of 'ChromatogramGraphic' is
> > > > > > totally
> > > > > > different than that of from ACE file.
> > > > > > Refer to image (2) ; you can see the two sequences generated by
> > > > > > same AB1
> > > > > > file is different in lenght also.
> > > > > >
> > > > > > What could be the problem here? Any suggestions please
> > > > > >
> > > > > > thanks in advance.
> > > > > > umanga
> > > > > > _______________________________________________
> > > > > > Biojava-l mailing list  -  [EMAIL PROTECTED]
> > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > > > > >             
> > > > > >             

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