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GT 11A Import BAM Files using Training Data

In order to get used to the operation of GT, we will use BAM import mechanism and operation using training data.

This BAM file is the assembly result of NGS lead by Velvet.

Operation

Start GT.

In the initial state, the main window is displayed as follows.

Right-click on the Root node in the TREE pane.

The menu will be displayed.

Select Expand All.

All nodes in the TREE pane are expanded.

Use the top "bam_importing".

Right click on the "bam_importing" node.

The menu will be displayed.

Select New Analysis Node -> Importing.

The BAM - Importing dialog will be displayed.

Click Add.

The "Add BAM Files (s)" dialog is displayed.

Click Ref ... and select the BAM file in the demo data area.

Click "Set".

Return to the BAM - Importing dialog.

Check all check boxes.

Click Set.

A Start Importing confirmation message is displayed.

 

Click "Yes".

Execution of the import starts and a progress message is displayed.

When the import is completed, a completion message is displayed.

Bam_importing node in the TREE pane A new import node is created.

Click on the new node to expand it.Right click mouse over Velvet node.

The menu will be displayed.

Select "Show BAM Information".

The BAM Information dialog will be displayed.

Click the tab to switch the panes.

Right click mouse over Velvet node.

The menu will be displayed.

Select "Show Read Alignment". The Alignment Viewer is displayed.

The Alignment Viewer can be resized.

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