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 - [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
