> 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/correlation-engine/reference/faq/rna-seq-alignment.md).

# RNA-Seq Alignment Conversion to Biosets

This guide explains how to prepare the output of the BaseSpace RNA-Seq Alignment application for import into Correlation Engine.

<figure><img src="https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-ee80908fa212f6f4a396404311dba93180f1dbfb%2FRNA-alignment.png?alt=media" alt=""><figcaption></figcaption></figure>

## Source File

From the RNA-Seq Alignment analysis, navigate to the **FILES** view in your analysis. Under the `counts` folder, select the `*.genes` file to download.

## Transformation Steps

### Step 1: Add Column Headers

Edit the downloaded file by adding column headers to the first and second columns:

| Column                     | Header            |
| -------------------------- | ----------------- |
| First (gene identifiers)   | `Gene name`       |
| Second (expression counts) | `Test expression` |

### Step 2: Filter Empty Rows

Remove any rows where `Test expression` = 0.

### Final File Format

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

## Notes

* When using gene symbol identifiers, verify the correct species is assigned at the verification step during upload.
* Using unique RefSeq or Ensembl identifiers ensures the application recognises the correct species automatically.
* Any rows above the column names are treated as free-text header space — use this area to include information about the data (visible in the application after upload).
* This file type does not include fold change or statistical columns; CE will rank features by expression level. For differential analysis results (fold change + p-value), use the RNA-Express conversion workflow instead.


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