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?
This is your post at Gitter, correct? 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:
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
- Extended Help for Differential Expression Analysis Tools
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.