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[Biojava-l] Question about AB1 parser (ABIFChromatogram) Ashika Umanga Umagiliya Tue Jun 16 03:00:23 2009

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

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