> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/basespace/biosamples/associating-bs-data-w-projs.md). # Associating Biosamples with Projects When aggregating data for analysis BaseSpace Sequence Hub limits the scope to include only data from biosamples that are associated with the same default project. The method to associate data depends on how the biosample or data files are added. ### Associating Data With an Existing Biosample If the biosample name and project name for incoming data match to a biosample and project combination in your workgroup, BaseSpace Sequence Hub associates incoming data with the specified biosample. If the names cannot be matched to an existing biosample and default project, BaseSpace Sequence Hub creates a new biosample in the specified project or a new project if the specified project does not exist. * Sequencing run sample sheet—Specify the biosample name in the sample ID column and the default project in the Project column. * Biosample workflow file—Specify the biosample name and default project. * FASTQ upload—Select the project. * FASTQ upload using the CLI—Use the project flag to specify the default project. {% hint style="info" %} The biosample can be associated with a different default project than the one you are uploading to. BaseSpace Sequence Hub aggregates biosample data by associated project even when the files are stored in a different project. {% endhint %} ### Associating Data With a New Biosample or Project Biosample names must be unique within the project but can match the names of biosamples associated with other projects. * Sequencing run sample sheet—Specify a new biosample name in the sample ID column or a new default project in the Project column. * Prep tab—Specify the project name when the biosample is created or imported. * Biosample workflow file—Specify a unique combination of biosample name and default project. * CLI—Specify a unique biosample name in the project. * FASTQ upload—Specify a unique combination of biosample name and default project. * FASTQ upload using the CLI—Use the project flag to specify a new project. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/basespace/biosamples/associating-bs-data-w-projs.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.