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

Ashika Umanga Umagiliya aumanga at biggjapan.com
Wed Jun 17 02:49:46 UTC 2009

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,

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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