RNA STAR : -- genomeDir not available at UseGalaxy.org -- Resolved

usegalaxy.org support
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1

Hello,

I am following a Galaxy tutorial → Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics – and have run into an error. While using RNA STAR, the option to “Select reference genome” drop down arrow is not functioning properly. Can you please advise. Attached is an image illustrating the issue.

Galaxy_Assignment_Annotated
Galaxy_Assignment_Annotated2558×1038 477 KB

Thanks,
Z

2

Hello @zwyoas

There were server issues yesterday at Galaxy Main https://usegalaxy.org leading to server-side errors (across tools), and more work has been occurring overnight and continues through now. Meaning: even jobs successfully submitted may fail for server-side reasons, or have an extended queue time then eventually fail. It is best to wait a bit for that process to complete before rerunning.

We are investigating whether the problem with RNA-Star not locating indexed reference genomes is related or not.

More feedback soon.

Thanks for reporting the problem!

3

jennaj,

Thank you for the response.

After searching for a workaround, the reference genomes can be accessed in RNA STAR versions 2.5.2b-0 and 2.6.0b-1, but not 2.7.2b. Hopefully this helps debugging the issue.

Cheers,
~Z

4

Update:

The most current version of the tool has more reference genomes added at UseGalaxy.org: RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.5b)