# Uploading A. thaliana reference genome to RNA STAR

**URL:** <https://help.galaxyproject.org/t/uploading-a-thaliana-reference-genome-to-rna-star/4932>\
**Category:** usegalaxy.org support\
**Tags:** reference-annotation, custom-build, troubleshooting, custom-genome, reference-genome\
**Created:** [November 30, 2020, 10:07pm UTC](https://help.galaxyproject.org/t/uploading-a-thaliana-reference-genome-to-rna-star/4932 "2020-11-30T22:07:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ahu213](https://avatars.discourse-cdn.com/v4/letter/a/ce7236/32.png) [@ahu213](https://help.galaxyproject.org/u/ahu213)\
**Post date:** [November 30, 2020, 10:07pm UTC](https://help.galaxyproject.org/t/uploading-a-thaliana-reference-genome-to-rna-star/4932/1 "2020-11-30T22:07:54Z")

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I am using RNA STAR for analyzing paired-end Arabidopsis RNA data, however, the Arabidopsis genome is not one of the built-in reference genomes listed. Underneath this selection, it says “If your genome of interest is not listed, contact the Galaxy team (–genomeDir).” Where can I go to request the arabidopsis genome to be uploaded onto the RNA STAR tool?

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**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:** [November 30, 2020, 10:23pm UTC](https://help.galaxyproject.org/t/uploading-a-thaliana-reference-genome-to-rna-star/4932/2 "2020-11-30T22:23:27Z")

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Hi @ahu213

This is your post at Gitter, correct? [https://gitter.im/galaxyproject/Lobby?at=5fc523ea9af4396683ccca8e](https://gitter.im/galaxyproject/Lobby?at=5fc523ea9af4396683ccca8e)

You can upload the genome in fasta format and use it as a custom genome with any tool that also incorporates built-in indexes. Some tools require that a “database” is assigned, but you can do that too by promoting the custom genome to a custom build.

All that is what was discussed in Gitter, but perhaps you don’t know how?

This forum has much Q&A about the topic – I added some tags to your post to help you find those.

And these FAQs explain the steps exactly. The important part is deciding on a reference annotation at the same time that you decide on a reference genome, then making sure the format is a match. Full details are included below:

> **[Galaxy Support](https://galaxyproject.org/support/)**

- [Preparing and using a Custom Reference Genome or Build](https://galaxyproject.org/learn/custom-genomes/)
- [Mismatched Chromosome identifiers (and how to avoid them)](https://galaxyproject.org/support/chrom-identifiers/)
- [Extended Help for Differential Expression Analysis Tools](https://galaxyproject.org/support/diff-expression/)

We’ll be indexing more genomes in the future, and possibly paired reference annotation, but that is still a work in progress. Use a custom genome/build for now.

Thanks!