Local Run Manager is the integrated run planning and analysis software for Illumina benchtop sequencers, and is also available for off-instrument installation and analysis of benchtop sequencing data. Local Run Manager can create FASTQ files for index reads along with the data reads, though it does not create them by default. To configure analysis module(s) used by Local Run Manger to generate FASTQ files for index reads, follow the steps below:

Note: Due to the modular nature of Local Run Manager, these changes must be made for every analysis module for which you want to generate FASTQs for index reads. This is not a global framework setting.

1. Navigate to the Local Run Manager analysis module folder:
   1. Frameworks versions 1 and 2: C:\Illumina\Local Run Manager\Modules\{module}\{version}
   2. Framework version 3: C:\Program Files\Illumina\Local Run Manager\Modules\{module}\{version}
2. Edit the file IsisConfigSettings.tsv in a plain text editor like Notepad.
   1. Note: If you receive permissions errors editing or saving the file, run Notepad in Administrator mode.
3. Add a line and enter the value CreateFastqForIndexReads, enter tab, and then enter the value 1
   The line should look like below, where the arrow indicates a tab:
   
   Note: The option is case sensitive and must be entered exactly as written.
4. Save the IsisConfigSettings.tsv file, making sure it remains a tab-separated value text file. Restarting the Local Run Manager services is not necessary.

For all analyses performed by the Local Run Manager analysis module with this confirm change, a FASTQ file is generated for each index read for each sample. To turn off this function and revert to the default FASTQ generation behavior, change the value in the CreateFastqForIndexReads line from 1 to 0, or delete the line, and save the file.