[Bioperl-l] Traces as X, Y coordinates

[SRMD, Col - Underwood, Anthony]

Hi there,

Please does anyone have experience with using the Bio::Seq::SequenceTrace
and Bio::SeqIO::scf modules to extract peak values for the different traces
(G,A,T and C) which can then be plotted using a graphics module along with
the bases themselves at the appropriate positions. I'm a little unclear as
to how the trace, peak indices, peak_index_at, base_at etc methods work.

If someone has exprience in how to go from an scf file to arrays of values
which represent x, y coords and bases, quality at each x coord then I'd
really appreciate your advice and insight.

Many thanks,

Anthony

Dr Anthony Underwood
Bioinformatics Group
Genomics, Proteomic and Bioinformatics Unit
Central Public Health Laboratory
Health Protection Agency
61 Colindale Avenue
London
NW9 5HT
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: anthony.underwood at hpa.org.uk