> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/correlation-engine/reference/faq/cufflinks-output.md).

# Cufflinks Assembly & DE Output Conversion to Bioset

This guide explains how to transform the output of the BaseSpace Cufflinks Assembly & Differential Expression application into a bioset file for import into Correlation Engine.

![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-ba5c7102db6070649ddc9e4c762d54deadab0228%2F0%20\(1\).png?alt=media)

## Source File

The most straightforward method is to use the **Gene Browser** section within the Cufflinks app:

1. Set the **Significant** filter option to `True` (applies a q-value cutoff of 0.05).
2. Click **Save Filtered Table** at the bottom of the page.

Saving an unfiltered version first is advisable if you want to perform an FDR analysis to determine whether a bioset should be tagged as "Below threshold significance."

### Example File Content

| Test ID | Gene    | Locus                   | Status | log2(TestFPKM) | log2(CtrlFPKM) | log2(Ratio) | q Value  | Significant |
| ------- | ------- | ----------------------- | ------ | -------------- | -------------- | ----------- | -------- | ----------- |
| A2ML1   | A2ML1   | chr12:8975149-9029381   | OK     | 0.73           | -10            | -10.73      | 1.68E-04 | TRUE        |
| ABHD12B | ABHD12B | chr14:51338877-51371688 | OK     | -1.52          | -10            | -8.48       | 1.68E-04 | TRUE        |

## Transformation Steps

### Step 1: Extract and Rename Columns

| Original Header        | New Header           | Transformation                                                             |
| ---------------------- | -------------------- | -------------------------------------------------------------------------- |
| `Gene`                 | `Gene name`          | None                                                                       |
| `log2(Ratio)`          | `Log2 fold change`   | Remove values between -0.2630344 and +0.2630344 (equivalent to ±log₂(1.2)) |
| `log2(<Test> FPKM)`    | `Test expression`    | Un-log: 2^value                                                            |
| `log2(<Control> FPKM)` | `Control expression` | Un-log: 2^value                                                            |
| `q Value`              | `q-value`            | None                                                                       |

The FPKM column headers vary based on the test and control group names you specified. CE biosets report FPKM values in unlogged format, so the transformation to 2^value is recommended for consistency.

### Step 2: Apply Fold Change Cutoff

Since the q-value cutoff was already applied by the Significant filter, the remaining quality step is the fold change cutoff. Remove rows where `log2(Ratio)` is between -0.2630344 and +0.2630344.

### Step 3 (Optional): Rename Gene Names to RefSeq Identifiers

CE matches RNA-seq biosets to the correct platform model using species-specific RefSeq identifiers. Skipping this step results in the bioset being treated as a custom platform. Mapping files are available for human, mouse, and rat.

{% hint style="info" %}
Not all genes in the Cufflinks output will be recognised by CE gene tables — some miRNAs and lincRNAs may not map.
{% endhint %}

### Step 4: Add Header Information

Add a free-text header above the data table:

```
Bioset summary = <study title>
Comparison = <test group> v. <control group>
Data pre-processing = FASTQ files were downloaded from Sequence Read Archive (SRA). No other preprocessing was performed.
Analysis summary = <alignment genome, software used, gene identifiers, cutoffs applied>
Test expression - Median FPKM expression in <test group> (total replicates = N)
Control expression - Median FPKM expression in <control group> (total replicates = N)
Internal ID - <GSE number>
```

### Step 5: Import

Import the final bioset through the CE Import UI. Select ranking on **absolute fold change, descending**.

## Final File Format

```
Bioset summary = <title>
Comparison = <test> v. <control>
...
Gene name    Fold change    Control expression    Test expression    q-value
A2ML1        -10.73         1.66                  0.00               1.68E-04
ABHD12B      -8.48          0.35                  0.00               1.68E-04
```


---

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