# RNAstar genome not available? Use a custom reference genome!

**URL:** <https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062>\
**Category:** usegalaxy.eu support\
**Tags:** custom-genome, mapping, reference-genome, tool-help, rna\_star\
**Created:** [December 3, 2024, 10:26pm UTC](https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062 "2024-12-03T22:26:16Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![drcottoncandy](https://avatars.discourse-cdn.com/v4/letter/d/6bbea6/32.png) [@drcottoncandy](https://help.galaxyproject.org/u/drcottoncandy)\
**Post date:** [December 3, 2024, 10:26pm UTC](https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062/1 "2024-12-03T22:26:16Z")

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Hi Everyone,  
I am working with a very niche insect species and I am trying to perform RNAseq analysis using SRA files from NCBI. I have gotten to the point in the RNAseq training where I now have to map the RNAseq files to the organismal genome. I have been able to retrieve the GTF file of the species genome from NCBI, and now I am trying to use RNAstar. My issue is that once I have selected : use genome reference without builtin gene-model but provide a gtf (as per the instructions provided by the tutorial) I am unable to find my species in the organism genome dropdown. I am prompted to contact the Galaxy team (–genomeDir), but I am also not sure how to do that so I am reaching out here in hopes that someone can help me with either finding out how to contact them, or being able to run RNAstar. Here is what my issue looks like :

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/e1c0f4dc6424d36f9430bb2e7f169b561c752e6a.png)  
I hope to hear from someone soon!  
thank you all 🙂

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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:** [December 4, 2024, 6:32pm UTC](https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062/2 "2024-12-04T18:32:02Z")

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Welcome, @drcottoncandy

You can get both the reference genome and the reference annotation from NCBI, load those into Galaxy by URL, standardize the data formats (RNA STAR is picky about formats, so don’t skip this!), then select both datasets _from the history_ at runtime.

The example linked here was also from NCBI, so this should be really close to what you’ll want to do, too.

> [@reference genome for STARsolo](https://help.galaxyproject.org/t/reference-genome-for-starsolo/13627/2):
>
> You can use the **Custom Reference Genome** function for your genome. This will work just like native server index that happens to be available.
> 
> We had another question about this today where I provided all the details, plus a fresh example of the data preparation steps. This should work for you, too!
> 
> Please see → [Inquiry about lettuce genome](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608)
> 
> Other similar topics can be found with the tag #custom-genome
> 
> With more here → [FAQ: NCBI reference data](https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720)

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Please give that a try and let us know if you have any questions! 🙂

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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:** [April 21, 2026, 12:10am UTC](https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062/3 "2026-04-21T00:10:25Z")

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