RNA STAR error on trimmomtaic files

Hi @s.godbole

This error can be produced when options that require reference annotation are used, but no reference annotation is input.

Most likely, it was the option for Per gene/transcript output.

If you don’t have reference annotation yet for the mm10 genome, there are a few choices. One is UCSC in their downloads area (not from the Table Browser). Navigate to the file, then copy the URL and paste it into the Upload tool. This prior Q&A explains how to do this for another genome – but the method is mostly the same for any genome. You want mm10.

I added a few tags to your post that point to more Q&A. Genecode is another common annotation source for this genome build/version – just be aware that from that source you’ll need to remove the headers before using the dataset (this can be done is Galaxy, as explained in other posts).

Hope that helps!

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