Hi, Are you sure that the AB1 file actually contains more than 520bp? Have a check there first (using something like trev should display the AB1 processed data) and then we can see if its a problem in the data or the program.
Andy Ashika Umanga Umagiliya wrote: > Greetings all, > > When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls > read is lower than the basecalls in a Phrap ACE file. > > For example I parse the AB1 file using biojava ABIChromatogram , it gave > the following basecalls: > > ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa > ttacttacacatatgttcttccctaataacagagttttacgatccgaag > accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg > gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt > tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg > gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata > agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat > tatccggtattagctccggtttcccgaagttatcccagtcttataggta > ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa > gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg > ttcatcctgagccaggatcaaactctccaa > > Total number is 520 , > > > But in Phrap ACE file the corrosponding entry is : > (should get compliment sequence to compare) > > RD 2008-10-24_A02_S_R.ab1 1404 0 0 > gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat > aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat > cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga > gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat > aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg > agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat > atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc > caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg > acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg > gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt > ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta > tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga > ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta > atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt > tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta > ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac > tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg > gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC > CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG > AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA > CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC > TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC > TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT > AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC > CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG > GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA > TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT > AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg > ttaa > > My question is why biojava parser only give 520 bases? Is there a way to > parse all 1404 bases as seen in Phrap ACE file? > > 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
