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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
