To specify the values for the Sequence Alignment step
1. Click Next or Alignment.
The Alignment Settings page opens. 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.
 | For a detailed discussion of the Sequence Alignment tool and its settings, see Sequence Alignment Tool. |
2. Leave the default values as-is, or make any changes as needed.
3. Do one of the following:
• To specify post-processing options for an alignment project, continue to To specify the post-processing options for a Sequence Alignment project.
• To finish the project, click Finish, and then continue to To finish the project.