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In order to use Trim adapters function, you will need to know the adapter sequences. To trigger the Trim adapters function, please select Unaligned Reads node and then select Trim adapters from the Pre-alignment tools section of the task pane. In the Trim adapters page (Figure 71), paste the adapter sequences into the textbox and select the  button.

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There are cases when the Trim adapters function does not work properly, for example: the existence of N's base in the read, etc. Therefore, there are advanced options which allows user to configure how the matching is done to trim adapter sequence. The advanced options dialog box is shown in Figure 82.

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