Trimming using the Trim tool

Sequence reads can be trimmed based on a number of different criteria. Using a trimming tool for this is particularly useful if:

To start up the Trim tool in the Workbench, go to the menu option:

        Toolbox | Molecular Biology Tools (Image lab_work_support) | Sanger Sequencing Analysis (Image assemblyfolder)| Trim Sequences (Image trim)

This opens a dialog where you can choose the sequences to trim, by using the arrows to move them between the Navigation Area and the 'Selected Elements' box.

You can then specify the trim parameters as displayed in figure 19.5.

Image trimstep2
Figure 19.5: Setting parameters for trimming.

The following parameters can be adjusted in the dialog:

Click Finish to start the tool. This will start the trimming process. Views of each trimmed sequence will be shown, andyou can inspect the result by looking at the "Trim" annotations (they are colored red as default). Note that the trim annotations are used to signal that this part of the sequence is to be ignored during further analyses, hence the trimmed sequences are not deleted. If there are no trim annotations, the sequence has not been trimmed.