Adapter trimming
Clicking Next will allow you to specify adapter trimming.
The CLC Genomics Workbench comes with a set of predefined adapter sequences from the most common kits provided by the high-throughput sequencing vendors. You can easily add or modify the adapters on this list in the preferences:
Edit | Preferences (
) | Data
This will display the adapter trim panel as shown in figure 23.2 where each row represents an adapter sequence including the settings used for trimming.
Figure 23.2: Editing the set of adapters for adapter trimming.
At the bottom of the panel, you have the following options:
- Add Default Rows. If you have deleted or changed the pre-defined set of adapters, you can add them to the list using this button (note that they will not replace existing adapters).
- Delete Row. Delete the selected adapter.
- Add Row. Add a new empty row where you can specify your own adapter settings.
All the information in the panel can be edited by clicking or double-clicking. The Strand, Alignment score and Action settings can also be modified when running the trim (see figure 23.8).
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