> 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/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/split-matrix.md).

# Split matrix

Split matrix can be invoked on any counts data node with more than one feature type. For example, a CITE-Seq experiment would have Gene Expression counts and Antibody Capture counts in the single cell counts data node. Datasets generated by [10X Genomics' Feature Barcoding](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc) experiments also utilize this task to split different feature measurements for downstream analysis.

There are no parameters to configure, to run:

* Click the counts data node you want to split
* Click the **Pre-analysis tools** section of the toolbox
* Click **Split matrix**

The Split matrix task will run and generate output data nodes for each of the feature types. For example, if there are Antibody Capture and Gene Expression feature types in the input, Split matrix will generate two data nodes (Figure 1). Every sample is included in both matrices.

<figure><img src="https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a0c3533adf01d8940c0906d7846d979f83963768%2Fsplitmatrix.png?alt=media" alt="" width="489"><figcaption><p>Figure 1. Split matrix generates separate data nodes for each feature type in the input matrix</p></figcaption></figure>

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


---

# 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/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/split-matrix.md?ask=<question>&goal=<user_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.
