# How to use the 'OverrideCycles' setting in the Run Planning User Interface **Background** The OverrideCycles setting is used to change the way a read or part of read is treated by BCL Convert. The BCL Convert app for onboard DRAGEN or BaseSpace requires a v2 sample sheet, which can be made using Run Planning on select platforms or in BaseSpace. See [Sample Sheet page](https://help.connected.illumina.com/run-set-up/overview) for links to additional details on required and optional field inputs for v2 Sample Sheets. *Key arguments for Override Settings* * **Y** - Use data in Read cycles * **U** - Use data as UMI cycles * **I** - Use data as Index cycles * **N** - Do not use data in either Read or Index *Setting Override Cycles in Run Planning* * The Run Planning UI is available in the Control Software on the MiSeq i100 Series and NovaSeq X Series instruments. * BaseSpace allows for 'OverrideCycles' designation during the Run Planning sample sheet setup. Run Planning with Onboard DRAGEN ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-3b8394a0310e316ca314494139e61d1f15102754%2Fimage1.png?alt=media) Run Planning with BaseSpace ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-ab1c4dc73df0114bdd88458fd9a0c7e0ffcc672f%2Fimage2.png?alt=media) * The 'OverrideCycles' defaults in Run Planning will match the run setup as applicable: Y(Read 1); I(Index 1); I(Index 2): Y(Read 2). ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-444e0f15ef1b34438b3e39a385470ba7c7015e5e%2Fimage3.png?alt=media) To skip cycles in either the Read or Index: * Designate the appropriate cycles with the mask flag "N." * For example, mask the first cycle of each Read for Illumina Stranded RNA libraries using N1Y150 for Reads 1 and 2. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-e34c7576142e66d1c8d151c7c49831b29ce0f946%2Fimage4.png?alt=media) If the Index read includes a UMI portion: * Designate the appropriate cycles with 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. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-4b0edc4248533edfc814113f185e8b87067d2be8%2Fimage5.png?alt=media) To ignore an entire index while demultiplexing: * Use case includes demultiplexing runs that contain both single-indexed and dual-indexed samples * Remove the "I" from the 'OverrideCycles' setting for the index read that is to be ignored in the **\[BCLConvert\_Settings]** section. * Remove the column (including the column header) for the index read that is to be ignored in the **\[BCLConvert\_Data]** section. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-af4afc874774362d92d164d6af8925a247e5040d%2Fimage6.png?alt=media) ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-c987d710ba6bff4e43f1faece3a8b3c5540f897b%2Fimage7.png?alt=media) *Notes for Manual Sample Sheet Modification* * **\[Reads]** section: This must contain the cycle numbers designated in the RunInfo.xml file (including the cycles to be ignored or treated differently). ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-568d9b69887af864b5726b901c24f359742ef2a2%2Fimage8.png?alt=media) * **\[BCLConvert\_Settings]** section: This must contain the appropriate 'OverrideCycles' setting. * In this example, a sequencing run was completed with 16 cycles for the i5 index, but the actual index for a subset of samples is only 8 bp. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-8445f765057a1f8ec75767752fc0127a0f08f056%2Fimage9.png?alt=media) * * For some instruments that specify the i5 index in the Reverse Complement orientation, the 'N' is at the beginning of the i5 index (example: Y150;I8;N8I8;Y150). For more information, see [Guidelines for reverse complementing i5 sequences for demultiplexing](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001800). * **\[BCLConvert\_Data]** section: This section contains the correct indexes. * If some index cycles are ignored/treated differently, then this section should contain the correct, shortened indexes. * Ns are not recognized as wildcard characters. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-b327b7d3c3142d9be5184d0efd137364874a234f%2Fimage10.png?alt=media) More information about this setting can be found in the BCL Convert online help [page](https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/BCLConvert/SampleSheets_swBCL.htm). \ \ \
| | | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5671), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001800%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |