Reference genome not loading in RNA Star

I agree with @igor – and from what I can see, none of the other UseGalaxy servers host the reference genome with the special tutorial reference annotation built in the same as the UseGalaxy.no server.

I can see that you got this working, but for anyone else running into this same issue:

The annotation changes more frequently that the assembly, so people like to supply their own. Any source of human reference annotation that is also based on the GRCh38/hg38 assembly will work, especially for a tutorial. Later on when working on real data, you can learn about the different sources, choose the best content for your project, and make minor changes to help with technical compatibility (format tuning, not content).

We have some guides

  1. FAQ: Extended Help for Differential Expression Analysis Tools

    Scroll down to the section about reference data.

  2. Reference genomes at public Galaxy servers: GRCh38/hg38 example

    When using the built-in native genome for hg38 at UseGalaxy.org, the NCBI RefSeq annotation hosted by UCSC would be a good choice. Simple format, curated content, based on the correct base assembly.

  • FAQ: Working with GFF GFT GTF2 GFF3 reference annotation (linked from the guide above)
    UCSC annotation
    • Find annotation under their Downloads area. The path will be similar to: https://hgdownload.soe.ucsc.edu/goldenPath/<database>/bigZips/genes/
    • Copy the URL from UCSC and paste it into the Upload tool, allowing Galaxy to detect the datatype.

Getting a custom genome and annotation paired up is also possible (and it looks like you were able to do this!), but I think just getting the annotation the first time is a bit easier. :slight_smile: