Automatic trimming

Sequence reads can be trimmed automatically based on a number of different criteria. Automatic trimming is particularly useful in the following situations:

To trim sequences automatically:

        select sequence(s) or sequence lists to trim | Toolbox in the Menu Bar | Molecular Biology Tools (Image lab_work_support) | Sequencing Data Analysis (Image assemblyfolder)| Trim Sequences (Image trim)

This opens a dialog where you can alter your choice of sequences.

When the sequences are selected, click Next.

This opens the dialog displayed in figure 18.5.

Image trimstep2
Figure 18.5: 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.