Adapter trimming

Clicking Next will allow you to specify adapter trimming.

In order to trim for adapters, you have to create an adapter list first to be supplied to the trim tool in this step:

        File | New | Trim Adapter List

This will create a new empty trim adapter list.

You can also create an adapter list by importing a csv or Excel file with the adapter information in the following format:

"Name";"Sequence";"Strand";"Alignment score";"Action"
"Adapter 1";"AAATTTGC";"Plus";"Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4";"Remove adapter"
"Adapter 2";"AAACGCCT";"Plus";"Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4";"Remove adapter"

At the bottom of the view, you have the following options:

Image trim-adapters
Figure 23.2: Adding a new adapter for adapter trimming.

The information to be added for each adapter is explained in the following sections, going into detail with the adapter trim. Once the adapters have been added to the list, it should be saved (Image save), and you can select it as shown in figure 23.8.



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