not sure this fits in the biojava-l, but I don't know where else to ask.
I am writing a java GUI that uses phred files (.phd.1 and .poly) to analyse sequences and find mutations. On .ab1 files Phred works nicely, but files from a CEQ2000 (saved as .scf) show very often inserted pseudo N or doubling of bases (e.g. GG i.o. G). Has anyone out there experience with Phred and Beckman .scf files?
The main differences I have noticed between the CEQ2000 and ABI3100 files are less variations between areas in the ABI as well as peak spacing of around 12 pix in the ABI vs 20 in the CEQ2000...
Thanks a lot,
david
here is an extract of inserted N in the middle of a sequence.
G 2222 35258.9974 0.941488 N -1 -1 -1 472.356505 98.422154 4532.105402 23.156642 A 2246 90044.20537 2.331656 N -1 -1 -1 10705.5386 42.180923 32.016443 271.750002 T 2264 55872.20905 1.243214 N -1 -1 -1 418.865077 57.245538 0 6615.988769 N 2276 -1 -1 N -1 -1 -1 38.078643 121.521231 0 633.40226 T 2286 15458.42054 0.33629 N -1 -1 -1 225.751957 131.564308 165.41829 1944.476831 N 2306 -1 -1 N -1 -1 -1 342.70779 177.762462 4757.109849 249.955516 N 2319 -1 -1 N -1 -1 -1 733.467202 300.288 471.353191 213.858398 G 2306 40290.91505 0.892624 N -1 -1 -1 342.70779 177.762462 4757.109849 249.955516 A 2328 62598.56983 1.390287 N -1 -1 -1 7399.949698 283.214769 124.50839 79.686091 A 2349 28561.70244 0.594684 N -1 -1 -1 3681.842162 99.426462 41.799245 34.053885 A 2369 27606.10982 0.61948 C 2385 3717.947077 0.076516 3552.193447 155.667692 100.496058 21.113409 A 2389 28438.40017 0.667774 N -1 -1 -1 3690.908505 361.550769 56.028776 90.583334 C 2406 57411.24923 1.369483 N -1 -1 -1 310.068953 6816.236308 118.282971 79.686091 A 2424 22989.52763 0.520666 T 2421 4193.395393 0.090929 3229.431613 241.033846 31.127098 493.781332 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
