Run setup modes for the MiSeq
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The run setup modes available depend on the version of the Windows operating system and MiSeq Control Software (MCS) installed.
(Terms: LRM = Local Run Manager, BSSH = BaseSpace Sequencing Hub, IEM = Illumina Experiment Manager)
MCS v2.6 or lower
There is only one run set up mode.
Provide a sample sheet during run setup.
Use IEM to create the sample sheet.
Data can be uploaded to BSSH.
MCS v3 and LRM v2
LRM Mode
Create the run in LRM.
Data can be uploaded to BSSH.
Sample Sheet Mode
In Sample Sheet mode, select the sample sheet from the control software. The sample sheet will be sent to Local Run Manager for validation and/or automatic run creation.
Local Run Manager secondary analysis can be disabled.
Use the to create the sample sheet (or create the sample sheet in LRM).
Data can be uploaded to BSSH.
Manual Mode
Set up the run in the control software.
BaseSpace Run Monitoring can be used.
Data cannot be saved in BaseSpace. BaseSpace Run Monitoring and Storage is not available (though Run Monitoring Only can be used in Manual Mode).
Toggle between modes during run setup (after selecting Sequence).
MCS v4 and LRM v3
LRM Mode
Create the run in LRM.
Data can be uploaded to BSSH.
Sample Sheet Mode
Import the LRM sample sheet into LRM to create the run.
Data can be uploaded to BSSH.
Manual Mode
Set up the run in the control software.
BaseSpace Run Monitoring or Run Monitoring and Storage may be used in Manual Mode - users may indicate these settings during run setup.
Toggle between modes during run setup (after selecting Sequence).
Note: When setting up a run in Sample Sheet Mode using LRM, LRM validates the sample sheet prior to the sheet being accepted. The Sample Sheet Header must have a valid Experiment Name and Workflow attached. All other fields in the sample sheet are optional, but if the user opts to fill in a field that overlaps with those provided in LRM, the input values will also be validated by LRM and may throw an error if LRM cannot interpret the values. If an Index kit is selected in the sample sheet, the index length for each sample must match that of the given kit.
Use the to locate templates (IEM-generated sample sheets will not work).
For any feedback or questions regarding this article (Illumina Knowledge Article #5572), contact Illumina Technical Support .