# I am using HISAT2, but my reference genome Rickettsia rickettsii is missing in the dropdown list.

**URL:** <https://help.galaxyproject.org/t/i-am-using-hisat2-but-my-reference-genome-rickettsia-rickettsii-is-missing-in-the-dropdown-list/12948>\
**Category:** Uncategorized\
**Tags:** custom-genome, mapping, custom-build\
**Created:** [July 11, 2024, 7:14pm UTC](https://help.galaxyproject.org/t/i-am-using-hisat2-but-my-reference-genome-rickettsia-rickettsii-is-missing-in-the-dropdown-list/12948 "2024-07-11T19:14:19Z")\
**Posts on this page:** 1\
**Showing post:** 2

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [July 11, 2024, 7:55pm UTC](https://help.galaxyproject.org/t/i-am-using-hisat2-but-my-reference-genome-rickettsia-rickettsii-is-missing-in-the-dropdown-list/12948/2 "2024-07-11T19:55:30Z")

</div>

Hi @Sonenshine

You can map to any reference genome that you want to within Galaxy. You can also create a custom database key to assign to datasets!

FAQ covered in this prior topic.

> [@Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at](https://help.galaxyproject.org/t/custom-genome-custom-build-how-to-use-a-genome-that-is-not-natively-indexed-at-the-server-you-are-working-at/10082/2):
>
> **For immediate use** , try using the **custom genome** feature.
> 
> [FAQ: How to use Custom Reference Genomes?](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html)
> 
> If you need to assign a **database** metadata to datasets, your custom genome can be promoted to a **custom build**.
> 
> [FAQ: Adding a custom database/build (dbkey)](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_add_custom_build.html)

If you are planning analysis that includes reference annotation, it is a good idea to also get that data at the same time, then to ensure that all the reference files work together. This other guide can be useful even if you are not doing differential expression analysis since it explains how tools use important data labels such as chromosome identifiers.

- [FAQ: Extended Help for Differential Expression Analysis Tools](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html)

Hope this helps! 🙂

---

_[View the full topic](https://help.galaxyproject.org/t/i-am-using-hisat2-but-my-reference-genome-rickettsia-rickettsii-is-missing-in-the-dropdown-list/12948)._