# RNA STAR problem: no options available for reference genome with built in index.

**URL:** <https://help.galaxyproject.org/t/rna-star-problem-no-options-available-for-reference-genome-with-built-in-index/8448>\
**Category:** usegalaxy.org support\
**Tags:** transcriptomics, reference-annotation, reference-genome\
**Created:** [August 10, 2022, 3:26pm UTC](https://help.galaxyproject.org/t/rna-star-problem-no-options-available-for-reference-genome-with-built-in-index/8448 "2022-08-10T15:26:21Z")\
**Posts on this page:** 1\
**Showing post:** 2

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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:** [September 21, 2022, 10:12pm UTC](https://help.galaxyproject.org/t/rna-star-problem-no-options-available-for-reference-genome-with-built-in-index/8448/2 "2022-09-21T22:12:18Z")

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Hi @ashleyf

Hopefully you have discovered this already, but public Galaxy servers usually do not include indexed reference annotation.

For the reference genome, try one of these:

- Use an available build-in reference genome index without annotation.

- Use a `fasta` file from the history that represents the reference genome.

For the reference annotation, try:

- Use a matching reference annotation provided by you from the history. `GTF` will work best with this tool and many others.

FAQs. Skip the first three and just review the last one if using a built-in genome index.

> [@Request for of Plasmodium species reference genome](https://help.galaxyproject.org/t/request-for-of-plasmodium-species-reference-genome/8702/2):
>
> - [working-with-fasta-datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/#working-with-very-large-fasta-datasets)
> - [reference-genomes](https://training.galaxyproject.org/training-material/faqs/galaxy/#reference%20genomes)
> - [adding-a-custom-database-build-dbkey](https://training.galaxyproject.org/training-material/faqs/galaxy/#adding-a-custom-database-build-dbkey)
> - [working-with-gff-gft-gtf2-gff3-reference-annotation](https://training.galaxyproject.org/training-material/faqs/galaxy/#working-with-gff-gft-gtf2-gff3-reference-annotation)

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_[View the full topic](https://help.galaxyproject.org/t/rna-star-problem-no-options-available-for-reference-genome-with-built-in-index/8448)._