Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

Performing a trim with default settings
You can specify how much dirty data should be trimmed off as a function of the number
of ambiguous base calls per run of bases by altering the Ends Trimming criteria. Each
pane in the End Trim window shows how much sequence should be trimmed off. There
will be a checkbox at an end if it requires trimming. Bases to be trimmed will be marked
in red.
You can proceed with the trim by clicking on the Trim Checked Items button. Once you
have trimmed your data dismiss the window with the command from the File menu called
Close Window.
Figure 6-1 The Ends Trimming button bar
Automatically selecting sequences for ends trimming
You can set the User Preferences so that sequence files are automatically added into the
trimming window as they are imported. During Import, Sequencher loads the sequences
that require trimming directly into the trim window. To determine which sequences
are directly imported into the trim window go to the Window menu and under User
Preferences click on Input/Output and then select the submenu File Import.
Figure 6-2 shows the criteria you use to specify which sequences are candidates for
direct import to the Ends Trimming window. (For more information see Chapter 21
“Customizing Sequencher and User Preferences”.)
Figure 6-2 User Preferences for setting trim criteria when files are imported
How to set the Ends Trimming criteria
The amount to be trimmed is based on the criteria you set for both the 5’ and 3’ ends of
the sequence. These criteria can be set independently of each other. To review or change
those criteria, go to the Ends Trimming window and click on the Change Trim Criteria
button. As you can see in Figure 6-3, you can trim off dye-primer peaks, set windows
of acceptable reliability, percentage of the highest peak height (3’ end) and even set an
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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