The clipping parameters will depend on the sequencing instrument, the chemistry, the laboratory, etc . The assumption is that, if the data produced is fairly consistent, then the measures drop and nonc can be used to define the clip points. To test if this is so, and to help select the parameters for trace_clip (see section trace_clip) we use the program scale_trace_clip. See section scale_trace_clip.
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. The first step in the procedure is for the user to select a representative set of readings and to employ trev to select clip points. These readings (which can be considered as a training set) are then used by scale_trace_clip to choose the parameters for trace_clip. For each reading it calculates the values of drop and nonc that would give the clip points closest to those selected by the user. Having analysed all the readings it calculates the mean of these drop and nonc values and then applies them, separately, to each of the readings again to measure the distance between the clip points they would give and those selected by the user. That is, it measures the errors in the clip points found using the mean cutoff values. From the ratio of the means of the two sets of errors it calculates the value fract_nonc. Finally scale_trace_clip applies the selected parameters to the readings again to calculate the errors they would produce if applied to the training set. Obviously a more satisfactory test is to apply the parameters to another set of readings that have been clipped by eye, or equivalently apply trace_clip to new readings and check its clip points using trev.
Given the variation in the data from different groups we make no claims as to the accuracy of the procedure.
Note that trace_clip also allows users to define base positions MIN_LEFT and MAX_RIGHT and the program will not produce a left clip point left of MIN_LEFT or a right clip point right of MAX_RIGHT. If users wanted to always clip at fixed points then MIN_LEFT and MAX_RIGHT can be used (with large values for nonc and drop) for this purpose.