To manually add amplicon regions
You can manually add as many amplicon regions as needed.
 | For detailed information about the format for a BED file, see BED file. |
1. For every region that you must add to the BED file, click Add.
A new amplicon region is displayed in the Amplicon Settings dialog box. As you add a new region, it is numbered sequentially. By default, the chromosome is set to M, and both the Start and End positions are set to “1,” but you can edit any or all these values.
2. As you manually add new amplicon regions, the following options are also available:
• Remove: Click to remove a selected amplicon region. You can remove only a single amplicon region at a time. After you remove a region, the remaining regions are automatically re-numbered.
 | No confirmation message is displayed before you remove a region, so be cautious when doing so. |
• Remove All: Click to remove all amplicon regions in a single step.
3. Leave Strict Sort Paired Reads selected, or optionally, clear the setting.
| | If Strict Sort Paired Reads is selected, then with paired reads, the start and end points for a paired read must match to the start and end points of the amplicon for the read to be assigned to the amplicon. In the event that a forward read that matches to Amplicon #1 extends into the reverse read that matches to Amplicon #2, this allows the assignment of the read to only one amplicon. |
4. Click OK.
The Open BED File dialog box closes. The New Project dialog box remains open.
5. Continue with setting up the new GeneMarkerHTS project.