Part A: Setting up preferences

To select a “working directory” for file output:

1. Data for all SeqNinja tutorials is located in the same .zip archive. Click here to download the SeqNinja tutorial data and extract the .zip archive to any convenient location (e.g., your desktop).

2. Launch SeqNinja if it is not already open.

3. Choose Edit > Preferences (Win) or SeqNinja > Preferences (Mac) and select Default Run Options from the list at left.

4. In the Default Run Options dialog, click the Browse button and navigate to tutorial data folder extracted in step 1.

5. Click OK (Win) or Open (Mac) to confirm the selected path.

6. After returning to the Default Run Options dialog, click Apply. Do not click OK at this point.

The new “working directory” will now be used during script execution as the default location for a !datapath* specified with a relative path, and also as the default location for files specified with a relative path, if no appropriate !datapath* is set.

*Note: Setting a preference for a “working directory” does not affect the directory shown by file choosers during the editing of scripts. File choosers instead show the last directory from which a file was chosen.

7. Next, select Editor from the list at left.

8. In the Editor dialog locate the checkbox next to Ask to save before running any script. By default, this box is checked, causing SeqNinja to prompt you to save each unsaved script before running it. You may choose whether to leave the box checked or unchecked.

*Note: In subsequent tutorials, you will be asked to save each script manually before running. Therefore, both options will allow you to follow the tutorials as written.

9. Click Apply and then OK.

Proceed to Part B: Inserting the bases.