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
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