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

additional control within the Trim Ends window. If you want Sequencher to ignore the
trim command for one or the other ends of the fragment(s) without modifying the overall
specifications, just click off the checkbox associated with that trim position.
Figure 6-4 shows a portion of the base detail for these sequences. You can double-click
on the sequence icon and invoke a Sequence Editor to examine the data in more detail.
Figure 6-4 Bases view in Ends Trim window
Sorting items
In order to assist you with the review of your data prior to trimming you can sort the
fragments. Click on the Sort Items button at the top of the Ends Trimming window to
order the fragments being trimmed. Figure 6-5 shows the sort criteria.
Figure 6-5 Sort Fragments dialog box
Executing the trim
Once you have reviewed your data and are happy with the criteria you have set, you
proceed with the trim by clicking on the Trim Checked Items button. Sequencher warns
you that this command cannot be reversed with the Undo command. To proceed, click
the Trim button. Any red lines or bases will disappear from the Ends Trimming window.
Now you can dismiss the window with the command from the File menu called Close
Window.
Remember to save your work at this point by going to the File menu and using the Save
Project command, since none of your trim work will have been recorded onto disk.
Alternatively use the Auto-Save function to save your work at user-defined intervals (see
Chapter 21 “Customizing Sequencher and User Preferences”).
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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