# RNA-Seq alignment conversion to Correlation Engine Biosets

There are two options to transfer data to Correlation Engine from the outputs of the BaseSpace RNA-Seq alignment app. One, you can download the entire analysis in the project page.

1. Navigate to the FILES view in your analysis
2. Under the counts folder, select the \*.genes file to download

<figure><img src="/files/sxQj28UcUKrOwnkkMtJ7" alt=""><figcaption></figcaption></figure>

3. Edit the file by adding the headers 'Gene name" and Test Expression to the first and second column respectively. Filter the data file to remove any rows with zero Test expression counts.

| Gene name    | Test expression |
| ------------ | --------------- |
| FAM41C       | 16              |
| LOC100130417 | 43              |
| SAMD11       | 228             |
| NOC2L        | 590             |
| KLHL17       | 33              |

Note:

1. When using gene symbol identifiers, check at the verification step during upload to make sure the correct species was assigned to your upload
2. Using unique refseq or ensembl identifiers will ensure the application recognizes the correct species
3. The import process will consider any rows above the column names as free-text space for any information the user wants to include about the data and will be viewable in the application


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/correlation-engine/correlation-engine-faq/rna-seq-alignment-conversion-to-correlation-engine-biosets.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
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.