If the Interactive clipping required? question is answered as
yes then the
trev (trace editor and viewer) program will be
used to display the trace files one at a time. (Note that this is the only
section of pregap that requires a graphics display.)
The viewer allows the quality clips for both the 5' and 3' ends to be set using the Edit menu and the left mouse button in the trace display.See section Trev. Alternatively if the trace is deemed to be of too low quality it may be rejected completely, in which case it will be added to the failure file of filenames.
Once happy with the quality clips for a reading, select Exit (or Reject) from the File menu and the next trace should appear. This is repeated until all have been processed.