[Biojava-l] Experience with Phred base calling on Beckman CEQ 2000?

[david atlan (PHENO)]

Hi,

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