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Functions and Operations of GenomeTraveler GT 11A Import BAM Files using Training Data
Functions and Operations of GenomeTraveler GT 11A Import BAM Files using Training DataGenome Analysis Software Info Site
Official Technology Information Site of in silico biology, inc.
Function Menu
License Activation
Function Overviews and Basic Operation
Work Bench
Feature Map- Feature Key and Feature
Management and Operations of Feature Keys- Attributes of Feature Keys
- IMC Original Set Feature Keys
- Types and Roles of Qualifiers
- IMC Original Set Qualifiers
- View and Edit Qualifiers
- Feature Position on Genome Sequence
- Feature Fragmentation
- Feature Synthesis
- Feature Fusion
- Feature Operators
- Link and Refer on Feature
- Feature Mapping
- Register, Edit, Delete Feature
- Feature Appearance
- Join and Delete Position
- Feature Categorization and Presentation
- Import Feature
- Export Feature
- Numbering of Feature
Sequence and Data Input and Output- Genome / Sequence Viewer / Editor
GenBank EMBL Viewer
Sequence Viewer
Annotation Viewer- Multiple Genome Viewer (Linear Map)
Circular Genome Viewer-Designer
Plasmid Map Viewer-Designer
Trace Viewer - Editor- Labeling and Coloring
- Description Window
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- Multiple Alignment Viewer
Phylogenetic Tree Viewer- GT Alignment Viewer
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Search Sequence and Annotation- Cloning
- Sequencing
- Gene and Genome Sequence Analysis
- Genome Annotation
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- Phylogenetic Tree
- Multiple Linear Genome Map
- Gene Cluster Alignment
Multiple Circular Genome Map
Dot Plot Analysis
Venn Diagram Analysis- Core Genome Analysis
- Global Genome Rearrangement Analysis
- Local Genome Rearrangement Analysis
- Mutation Analysis
- Enzyme Alignment by EC Number
- Unique Region Analysis
- Genome Mapping
- Expression Analysis
- Genome Design
Settings- Tools
- Window and Dialog Description
- What is "Do It Yourself" Genome Analysis Software?
- Functions and Operations of GenomeTraveler
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.
