scale_trace_clip -- a program to select parameters for trace_clip
-w winlen_nonc] [
-m max_right] [
-s start] file ...
scale_trace_clip is used to select parameters for the clipping
trace_clip. The clipping parameters will depend on the sequencing
instrument, the chemistry, the laboratory, etc so this program provides
a simple procedure to select appropriate values. Obviously the aim of
any automatic clipping routine like
trace_clip is to output clip points
that are close to those that would be chosen by visual inspection of the
traces. So the first step in the procedure is for the user to select a
representative set of readings and to employ
(see section Trev) to set clip
points. Next create a file of file names for the set of files and use this as
input to the program
The measures used by
trace_clip do not increase uniformly 5' to 3' but
scale_trace_clip finds, for each reading, the cutoff values for
each of the two calculations that give the closest position to that
chosen by the user. These cutoff values are accumulated for the whole
set of readings and their average computed. These averages become the cutoff
cut_nonc, cut_drop used by
scale_trace_clip uses the two cutoff values to
re-analyse the set of traces to find the amount of error produced by each. The
ratio of the two error totals provides the weighting value
nonc_fract used by
If selected, the procedure is followed for both ends of the sequence.
Once the parameters are calculated the program applies them to the set of input files and writes out the average error.
The file argument is a file of experiment file names.
The default arguments are
-w 101 -W 101 -R
See section ExperimentFile(4).See section trace_clip.