Why are there no available reference genomes in RNA-STAR?

[Sara_Cristina_Pinto]

Hey there,

I was trying to use the RNA-STAR tool in Galaxy to create read count files for my RNA-seq data since I do not have experience in bioinformatics, but there is no reference genome available. I am interested in the Arabidopsis thaliana TAIR10 genome and gene model, despite being present in other tools of Galaxy, it is not present in the RNA-STAR tool. Any sugestions in how to solve this problem?

Thank you!

[jennaj]

Welcome @Sara_Cristina_Pinto

Thank you for reporting the problem. The latest version of the tool wrapper, what was loading by default until a few minutes ago, requires some additional tuning. Ticket with details: https://github.com/galaxyproject/usegalaxy-playbook/issues/266

We have reverted to the two earlier versions at Galaxy Main https://usegalaxy.org. Galaxy EU has the updated version. Please refresh your browser window and reload the tool, at either. It has only 14 indexes so far (14 genomes) at Galaxy Main. Galaxy EU has 7 indexes. However, neither contain TAIR10, yet, but synching up more genomes across all usegalaxy.* servers is a priority project in progress.

What to do:

• Obtain and load the fasta version of the genome and use it as a Custom Reference Genome/Build at the Galaxy server you are working at. The exact same version of the genome indexed for other tools at this server can be found here:
  • http://datacache.galaxyproject.org/
  • Paste this link into the Upload tool: http://datacache.galaxyproject.org/indexes/Arabidopsis_thaliana_TAIR10/seq/Arabidopsis_thaliana_TAIR10.fa
  • Use the resulting fasta dataset as a Custom Genome “from the history” with this tool and others.
  • The genome will not need any additional re-formatting given the source link above (our version), but you may want to promote it to a Custom Build to be able to use your mapping results with tools that require an assigned “database” attribute.

FAQs:

• Preparing and using a Custom Reference Genome or Build
• How do I find, adjust, and/or correct metadata? (for how to assign your new custom build’s “database”)

Thanks again!

[jennaj]

Consolidating all related Q&A into a single topic: RNA STAR Reference Genome

Ongoing status will post to that topic along with related development tickets linked in it.