Start a Manual Run (Generate BCL Files)
Use the following instructions to start a sequencing run that only generates BCL files. Sample sheet is optional.
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Select Generate BCL files. |
The run name can only contain alphanumeric characters, spaces, dashes, and underscores.
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Select Single or Paired end for the read type. |
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Enter the number of cycles performed in each read: |
The total number of read cycles and index cycles cannot exceed the number of cycles specified by the reagent kit.
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Read 1—Enter the number of cycles for Read 1. |
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Index 1—Enter the length of the index read for Index 1. For a PhiX-only run, enter 0 in both index fields. |
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Index 2—Enter the length of the index read for Index 2. |
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Read 2—Enter the number of cycles for Read 2. This value is typically the same as the Read 1 value. |
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[Optional] Select your sample sheet. |
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8.
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Select Review, and then review your run. Configure the following optional run settings as needed: |
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If Read First sequencing is required, deselect the Sequence Indexes First checkbox. |
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If using custom primers, select the appropriate custom primers checkboxes. |
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If the instrument is connected to the cloud, and you are logged in with your BaseSpace Sequence Hub account, select a cloud run setting.
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To use a different output folder from the default, modify the output folder. You can change the default output folder in system settings. |
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Select a custom recipe file. |
