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

[Andreas Prlic]

Great that it works now!

Do you want to post some more documentation on the wiki page? We seem
to get queries regarding this every now and then so having more docu
might be helpful...

Cheers,
Andreas


On Wed, Jun 17, 2009 at 2:00 AM, Ashika Umanga
Umagiliya<aumanga at biggjapan.com> wrote:
> 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
>>>>>>>
>
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