# How to requeue FASTQ Generation using BCL Convert on BaseSpace BCL Convert on BaseSpace can be used to demultiplex (generate FASTQs) runs from any Illumina platform. If FASTQ generation cannot be requeued in BaseSpace Sequence Hub using the standard FASTQ Generation analysis or if there is a need to reanalyze using a different sample sheet or FASTQ generation workflow, BCL Convert app on BaseSpace can be used with a [v2 Sample Sheet](https://help.connected.illumina.com/run-set-up/overview#how-to-use-a-sample-sheet) as a solution. Using [Run Planning](https://basespace.illumina.com/run-planning/run-settings) (link requires BaseSpace login) is recommended to generate a v2 Sample Sheet for reanalysis to make sure that the required fields and formatting are correct. \*\*Creating a v2 Sample Sheet in [Run Planning](https://basespace.illumina.com/run-planning/run-settings):\*\*1. Create a v2 Sample Sheet using **Run Planning** in BaseSpace. This option can be found by selecting New Run on the BaseSpace Runs page. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-ff5067b7778660b0cf28ab677127b63d09d5813c%2Fimage1.jpg?alt=media) 2. **For Windows based instruments:** Select **NextSeq 1000/2000** as Instrument Platform, **BaseSpace** as the Analysis Location, and **DRAGEN BCL Convert** as Type of Analysis. Enter in the necessary library, index, and sample information, then select **Next**. **For Linux based instruments:** Select the instrument in which the run was performed as Instrument Platform, **BaseSpace** as the Analysis Location, and **DRAGEN BCL Convert** as Type of Analysis. Enter in the necessary library preparation and index kits, then select **Next**. 3. Add optional Adapter, select the Index Reads and Read Type, [Barcode Mismatch](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-troubleshooting-list/000002326/?utm_source=agent\&utm_medium=email\&utm_campaign=kb), [Override Cycles](https://knowledge.illumina.com/software/general/software-general-faq-list/000005671/?utm_source=agent\&utm_medium=email\&utm_campaign=kb) settings and input sample information (Sample ID, Index sequences\*\*\*\*\* and Project) on the Analysis Setup page to match the original Sample Sheet. Then select **Next**. 4. A Run Review page will be displayed from which users can select the option **Export** to download the new v2 Sample Sheet. If user selects **Save as Planned**, it will be listed as a Planned Run on BaseSpace. Return to the **Runs** tab and select **Planned**. Check the box next to the planned run, then select **File > Download > Sample Sheet**: ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-df716408a3d98325bb61b28302458451ef6d5973%2Fimage2.jpg?alt=media) ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-c4ac21f5420a546f5ee7e2aa9dbeecb66baef6cf%2Fimage3.png?alt=media) **\*BCL Convert on BaseSpace requires i5 sequences to be in the forward orientation** for most platforms. Consult Illumina Technical Support if in doubt. \*\*Uploading the v2 Sample Sheet to a Project:\*\*1. Go to the **Projects** tab and create a new project or select an already existing project to open it. Upload the Sample Sheet to the Project by selecting **File > Upload > Files** from within the Project. 2. Select the **Other** option under **Choose File Type**, drag and drop or browse files to select the downloaded v2 Sample Sheet under **Select and Review**, and select **Complete Upload**: ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-eb69826be7c8b79a200e05492f5bf11e983a0abd%2Fimage4.jpg?alt=media) \*\*Launch BCL Convert:\*\*1. Once the Sample Sheet is uploaded to the Project, navigate to the **Apps** tab, select **All Categories** in the dropdown menu, and launch the **BCL Convert app**: ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-f135ddbe8213983217bc4ea3cb54c7b731e22c4b%2Fimage5.jpg?alt=media) 2. Select the run to be requeued, then select the uploaded Sample Sheet option under the **Override Sample Sheet** section. Select **Launch Application** to start the analysis. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-3facebd8c53c432d99ac8e4857ecdf7c6670cf74%2Fimage6.png?alt=media) 3. Once the BCL Convert analysis completes, FASTQ files will be added to the **FASTQS** tab of the Project that was specified in during Run Planning, or to a Project with the run name if no Project was listed in the sample sheet. **Important Notes:** * Run names and Sample IDs in v2 sample sheets cannot contain spaces or special characters; use only letters, numbers, dashes, or underscores. * Projects can be designated for output data by using the ProjectName field in the **Cloud\_Data** section of the sample sheet. If no ProjectName value is set, then the output project will use the value from the RunName entry in the sample sheet header. * Manual edits to the exported sample sheet before use in the analysis are discouraged. Incorrect, missing, or unexpected entries can cause analysis failure. \ \ \
| | | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6472), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006472%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |