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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).
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