How to use the 'OverrideCycles' setting in BaseSpace

The OverrideCycles setting can be used to change the way a read/part of read is treated by BCL Convert. The BCL Convert app on BaseSpace requires a v2 sample sheet which can be made using Run Planning in BaseSpace.

Using Override Cycles in a v2 Sample Sheet Changes must be made to the following sections of the v2 sample sheet while using the 'OverrideCycles' setting.

• Key arguments for Override Settings: Y - Use as data read cycles, U - Use as UMI cycles, I - Use as index cycles, N - Do not use data read cycles

BaseSpace Run Planning Modification

• BaseSpace now allows for 'OverrideCycles' designation during the Run Planning sample sheet setup.

  
• The 'OverrideCycles' defaults in BaseSpace Run Planning to match the run setup as applicable: Y(Read 1); I(Index 1); I(Index 2): Y(Read 2).

  
• If the index includes a UMI portion, the appropriate cycles must be designated to the UMI flag "U."

  • For example, a run may have Index 1 with a UMI of 8 bases in a run setup of Read 1 150, Index 1 16, Index 2 8, Read 2 150. The Override Cycles would register as Y150;U8I8;I8;Y150.

  • 

Manual Sample Sheet Modification

• [Reads] section: This must contain the actual cycle numbers (including the cycles to be ignored or treated differently).

  
• [BCLConvert_Settings] section: This must contain the appropriate 'OverrideCycles' setting.

In this example, a sequencing run was set up with 16 cycles for the i5 index, but the actual index for a subset of samples is only 8 bp long.    

For some instruments that specify the i5 index in the Reverse Complement orientation, the 'N' would be at the beginning of the i5 index (Y150;N8;N8I8;Y150).  

• [BCLConvert_Data] section: This section contains the correct indexes; if some index cycles are being ignored/treated differently, then this section should contain the correct, shortened indexes. Ns are not considered as wildcard characters.

  

If an entire index were to be ignored while demultiplexing (eg, when demultiplexing runs with single-indexed and dual-indexed samples), there must be no column (including the column header) for this index read in the [BCLConvert_Data] section.

More information about this setting can be found in the BCL Convert online help page.

For any feedback or questions regarding this article (Illumina Knowledge Article #5671), contact Illumina Technical Support [e-mail].