[Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?

[Ashika Umanga Umagiliya]

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  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>             
>>>>>>