Scale_trace_clip

NAME

scale_trace_clip -- a program to select parameters for trace_clip

SYNOPSIS

scale_trace_clip [-w winlen_nonc] [-W winlen_drop] [-s start] file ...

DESCRIPTION

scale_trace_clip is used to select parameters for the clipping program 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 trev See section `Trev' in 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 scale_trace_clip.

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 values cut_nonc, cut_drop used by trace_clip. Next 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 trace_clip.

The file argument is a file of experiment file names.

The default arguments are -w 51 -W 51 -s 100

OPTIONS

-w winlen_nonc

Set the length for the non-called over called window to winlen_nonc This should be an odd number and the same as that to be used in trace_clip

-W winlen_drop

Set the length for the peak to trough window to winlen_drop This should be an odd number and the same as that to be used in trace_clip

-s start

Force the first window to start the calculations from position start in the sequence. This can be useful to avoid poor data at the 5' end of a sequence.

SEE ALSO

See section ExperimentFile(4).See section trace_clip.