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
_______________________________________________
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
