Sequence Alignment Tool Settings

NextGENe Online Help : Sequence Alignment Tool : Sequence Alignment Tool Settings

The Alignment Settings page is available by doing one of the following:

• Clicking Alignment in the Project Wizard.

• Clicking Process > Alignment Settings on the NextGENe viewer main menu. See NextGENe Viewer main menu.

If you open the Alignment Settings page from the NextGENe Viewer main menu, then the reference file that was used for the currently loaded project or the project application type determines the settings that are displayed on the page.

The alignment settings that are available on the Alignment Settings page for any application type other than Transcriptome with alternative splicing, STR analysis, or HLA depend on the type of reference file—fasta, GenBank, or preloaded—that was loaded for the project. See:

• Alignment settings – .fasta or GenBank reference file.

• Alignment settings – Preloaded reference.

• BAM Sample Files settings.

• Sample Trim settings.

• Mutation Filter settings.

• File Type settings.

• Other settings.

For a detailed discussion of the alignments settings that are available on the Alignment Settings page for the Transcriptome with alternative splicing application type, STR analysis application type, or HLA application type, see:

• Transcriptome Alignment Project with Alternative Splicing in the NextGENe Sequence Alignment Tool.

• STR Analysis Project in the NextGENe Sequence Alignment Tool.

• HLA Analysis Project in the NextGENe Sequence Alignment Tool.