Basic Application Operation
The following operations are often used in IMC.
- Load (read) the base sequence file and display the main feature map.
- Perform Keyword Search.
- Find the restriction enzyme recognition site.
- View the sequence from the reverse complement side.
- Perform homology search.
Please visit when using IMC for the first time.
Please read the following when using GenomeTraveler (GT) for the first time.
Sample data will be installed automatically when GT is started for the first time.
Using this sample data, you can practice the operation.
If sample data is not displayed, confirm the demo directory and change it to the root directory and it will be displayed.
Sample data includes the following.
BAM file import:
Contains the result of importing the BAM file used for assembly and mapping. Each fragment of the BAM file can be viewed with the Alignment Viewer.
Mapping (using LAST):
The reference genomic data and the result of mapping NGS lead using LAST on its genome are stored. You can browse and analyze the reference genome data by activating the IMC, and you can view and analyze the mapping by starting the Alignment Viewer. It is also possible to execute new mapping using the same NGS data.
Assembly (using OASES):
Contains the AFG file of assembly result of NGS lead using OASES. Convert this to a BAM file and start the Alignment Viewer. It is also possible to use the same lead and execute a new assembly.
Mapping (using SLIDESORT):
contains reference genomic data and results mapped using SLIDESORT on its genome. You can browse and analyze the reference genome data by activating the IMC, convert the mapping result to a BAM file, and view and analyze it with the Alignment Viewer. It is also possible to execute new mapping using the same NGS data.
Assembly (using Velvet):
The AFG file of assembly result of NGS lead is stored using Velvet assembler. Convert it to BAM file and start up Alignment Viewer. It is also possible to use the same lead and execute a new assembly.