Plan the Run

1 From the Plan Run page, click the Select Instrument drop-down arrow and select a sequencing system, either MiniSeq or NextSeq.
2 In the Name field, enter a name for the sequencing run.
3 [Optional] In the Reagent Barcode field, enter the barcode ID of the reagent kit used for the run.

Entering the barcode ID links the reagent kit to the run.

4 [Optional] Select Use Custom Primer options:
R1—Use custom primer for Read 1.
R2—Use custom primer for Read 2.
Index—Use custom primer for index reads.
5 Select a read type, either Single Read or Paired End.
6 Enter the number of cycles for each read in the sequencing run:
Read 1 Cycles—Enter a value up to 151 cycles.
Read 2 Cycles—Enter a value up to 151 cycles. This value is typically the same number of cycles as Read 1.
7 Review the indexing scheme for the run. To make changes, override the defaults as follows.
    a Select the Override default indexing scheme checkbox.
    b Click an indexing scheme:
      Single Index—Performs a run with 1 index read.
      Dual Index—Performs a run with 2 index reads.
      No Index—Performs a non-indexed run.
    c Enter the number of cycles for each index read:
      Index 1 Cycles—Enter the number of cycles required for the Index 1 (i7) primer.
      Index 2 Cycles—Enter the number of cycles required for the Index 2 (i5) primer.

Note

Indexing is required when sequencing multiple libraries.

8 Make sure that a pool is present.
9 Click 1 of the following buttons to continue:
Sequence—The run appears on the Planned Runs list with a status of Ready. The run becomes available from the control software of your sequencing system.
Save and Continue Later—The run appears on the Planned Runs list with a status of Planning. When you are ready to sequence, select the checkbox for the run and click Sequence. The run becomes available from the control software of your sequencing system.