Output Files and Folders

The MiSeq system generates three specific run folders for each sequencing run: MiSeqTemp, MiSeqOutput, and MiSeqAnalysis. The MiSeqTemp folder serves as a temporary working area for instrument processes like MCS and RTA, with its contents automatically deleted after 7 days. The MiSeqOutput folder stores primary analysis files generated by RTA and is used for further analysis. The MiSeqAnalysis folder is accessed by LocalRunManager for secondary analysis. The naming convention for these folders includes the date of the run, instrument number, and flow cell barcode. During sequencing, files like SampleSheet.csv and RunParameters.xml are copied to these folders, and various subfolders contain base call data, logs, and configuration files. Additionally, flow cells are divided into tiles, with each tile having its output file named based on the tile number. The specifics of file and folder naming can vary based on the MiSeq reagent kit and flow cell type used.