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 | Sequencing Data 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.

When the sequences are selected, click Next.

This opens the dialog displayed in figure 31.5.

Image trimstep2
Figure 31.5: Setting parameters for trimming.

The following parameters can be adjusted in the dialog:

Click Next if you wish to adjust how to handle the results. If not, click Finish. 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.