# Running DRAGEN Amplicon 3.10.4 on BaseSpace on a single sample type with a hg38 reference

The DRAGEN Amplicon app can be used to analyze DNA and RNA Amplicon samples. Information about this pipeline can be found in the [DRAGEN user guide](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/Amplicon_Pipeline.htm).

The latest version of the app, **3.10.4**, has an issue while launching **DNA or RNA samples (not both)** when:

1. A **custom BED file** and **a hg38 reference genome** are selected. The in-built Amplicon manifests were designed for hg19 and can only be used if a hg19 reference is selected in the app.
2. **Nirvana annotation** is **enabled** for **GRCh38.**

For instance when the user select only a DNA sample -

![](/files/f7v4W8epiuvIAhvzuNTa)

A similar error will be raised if the user only input a RNA sample.

Currently, there are two ways this error can be mitigated:

1. **Disable Nirvana** annotation.
2. Select **'Custom**' for the **Targeted Amplicons input** in **both the DNA and RNA sections** (even if only one type of sample is being analyzed).

* When analyzing **only RNA samples** (with a custom hg38 BED file), select '**Custom**' for the **Targeted Amplicons** input in the **DNA section**, and **choose a BED** file in the '**Custom Manifest File**' section (this can be the same BED file that was used with the RNA samples).

  ![](/files/grEmt3sBCHjLNu6H0OSn)
* If only analyzing **DNA** samples, it would suffice if the user choose '**Custom**' for the **Targeted Amplicons input** in the **RNA section** (not required to actually chose a custom BED file).

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                 |
| :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #7870), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007870%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# 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://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000007870.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.