2 Select Next.
3 Confirm run parameters.
u Run Name—Name of the run as assigned in BaseSpace.
u Library ID—Name of the pooled libraries as assigned in BaseSpace.
u Recipe—Name of the recipe, either NextSeq High or NextSeq Mid depending on the reagent
cartridge used for the run.
u Read Type—Single Read or Paired End.
u Read Length—Number of cycles for each read.
u [Optional] Custom Primers, if applicable.
4 [Optional] Select the Edit icon to change run parameters. When finished, select Save.
u Run parameters—Change the number of reads or number of cycles per read.
u Custom primers—Change the settings for custom primers. For more information, see
NextSeq
Custom Primers Guide (document # 15057456)
.
u Purge consumables for this run—Change the setting to purge consumables automatically after the
current run.
5 Select Next.
Enter Run Parameters (Standalone Configuration)
1 Enter a run name of your preference.
2 [Optional] Enter a library ID of your preference.
3 From the Recipe drop-down list, select a recipe. Only compatible recipes are listed.
4 Select a read type, either Single Read or Paired End.
5 Enter the number of cycles for each read in the sequencing run.
u Read 1—Enter a value up to 151 cycles.
u Read 2—Enter a value up to 151 cycles. This value is typically the same number of cycles as Read 1.
u Index 1—Enter the number of cycles required for the Index 1 (i7) primer.
u Index 2—Enter the number of cycles required for the Index 2 (i5) primer.
The control software confirms your entries using the following criteria:
u Total cycles do not exceed the maximum cycles allowed
u Cycles for Read 1 are greater than the 5 cycles used for template generation
u Index Read cycles do not exceed Read 1 and Read 2 cycles
6 [Optional] If you are using custom primers, select the checkbox for the primers used. For more
information, see
NextSeq Custom Primers Guide (document # 15057456)
.
u Read 1—Custom primer for Read 1.
u Read 2—Custom primer for Read 2.
u Index 1—Custom primer for Index 1.
u Index 2—Custom primer for Index 2.
7 [Optional] Select the Edit icon to change run parameters. When finished, select Save.
u Output folder location—Change the output folder location for the current run. Select Browse to
navigate to a network location.
u Purge consumables for this run—Change the setting to purge consumables automatically after the
current run.
u Use run monitoring for this run—Change the setting to use run monitoring in BaseSpace.
Document # 15046563 v04
For Research Use Only. Not for use in diagnostic procedures.
20
NextSeq 500 System Guide
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