How to demultiplex a run without using either the i7 index or the i5 index using bcl2fastq2

To demultiplex without the i7 (index 1) using bcl2fastq2, follow this instruction.

1. Keep the index column (i7) under the [Data] section blank in the sample sheet.

2. Add this command to bcl2fastq2 command line: --use-bases-mask y\,n\,i\,y\

This command specifies how to process each cycle:

• n: Ignore the cycle.

• Y (or y): Use the cycle.

• I (or i) : Use the cycle for an Index Read

Example Sample Sheet (note the index 1 column is blank).

Example command:

bcl2fastq --runfolder-dir {runfolder-location} --output-dir {new-output-folder} --use-bases-mask y\\*,n\\*,i\\*,y\\*    

Similar instruction will be applied when demultiplexing without the i5 (index 2) using bcl2fastq2.

1. Keep the index2 column (i5) under [Data] section blank in sample sheet.

2. Add this command to bcl2fastq2 command line: --use-bases-mask y\,i\,n\,y\

Example Sample Sheet (note the index 2 column is blank).

See the bcl2fastq2 user guide for more information.

For any feedback or questions regarding this article (Illumina Knowledge Article #3145), contact Illumina Technical Support [e-mail].