MiSeq Reporter is able to generate FASTQ files for index reads. It does not generate them by default. To configure MiSeq Reporter to generate FASTQ files for index reads, follow the steps below:

Note: This procedure requires restarting the MiSeq Reporter Service, which requires administrative privileges on the computer. If you do not have administrative privileges, restarting the computer also restarts the MiSeq Reporter service.

1. Navigate to C:\Illumina\MiSeqReporter
2. Make a backup copy of MiSeq Reporter.exe.config
3. Edit the original MiSeq Reporter.exe.config using Notepad
4. Add the following to the top portion of the file (in the <appSettings> section):
   <add key="CreateFastqForIndexReads" value="1" />
5. Save the file
6. Restart the MiSeq Reporter service
   1. Start the Windows Task Manager by pressing Ctrl-Alt-Delete on the keyboard and then selecting Start Task Manager
   2. Select the Services tab
   3. Find MiSeqReporter on the list of services
   4. Right-click on MiSeqReporter and select Stop Service
   5. Right-click on MiSeqReporter again and select Start Service

For all analyses performed by MiSeq Reporter after making this change, a FASTQ file is generated for each index read for each sample. To turn off this feature (ie, to revert to the default behavior of MiSeq Reporter), change the value in <add key="CreateFastqForIndexReads" value="1" /> from 1 to 0, then restart the MiSeq Reporter service.