[Biojava-l] Question about AB1 parser (ABIFChromatogram)

[Andy Yates]

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
> 
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