Run Folders

Each run on the MiSeq generates three run folders, each with a specific purpose:

•

D:Illumina\MiSeqTemp—When the run begins, a temporary run folder is written to the local drive of the instrument computer and used as a working area for MCS and RTA. There is no need to access the MiSeqTemp folder. Contents of this folder are deleted after 7 days.

•

D:\Illumina\MiSeqOutput—RTA copies files from the MiSeqTemp folder to the MiSeqOutput folder. As primary analysis files are generated, RTA copies files back to the MiSeqTemp folder and populates the MiSeqAnalysis folder. Focus images and thumbnail images are not copied to the MiSeqAnalysis folder. Refer to RTA Folders and Files.

•

You can change the location of the output folder in the Output Folder field on the System Settings screen. For more information, refer to Set Default Folder Locations.

•

D:\Illumina\MiSeqAnalysis—When analysis by RTA is complete, Local Run Manager accesses the MiSeqAnalysis folder on the instrument local drive to begin secondary analysis. All files written to the MiSeqAnalysis folder are copied back to the MiSeqOutput folder. For more information, refer to MiSeqOutput Folder Contents.

If you are using BaseSpace Sequence Hub for analysis without replicating analysis locally, the MiSeqAnalysis folder on the instrument local drive is empty.