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.
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.