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

[Ashika Umanga Umagiliya]

HI Andy,

Thank you for the tip. I checked the AB1 with 'trev' and it gave the 
number of bases as 520.
But I wonder in Phrap ACE file how it show 1404 bases.

Best Regards,
Umanga

Andy Yates wrote:
> 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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