How to use a gtf file from ensemble?

I want to use a gtf file of Solanum_lycopersicum that I get from here. But when I choose it in the RNA STAR tool, (Unavailable) appears. How can I fix the problem?

Hi @Maryam_Momeni

Try getting the standard full GFF3 file instead. This will usually be from the website instead of the downloads area for Ensembl.

Get the reference genome, reference annotation, and reference transcriptome (if using) all at the same time. Then, standardize the formats at the very start. Put those prepared files in a distinct history. Make copies into histories that you plan to do analysis in. That keeps your master reference files someplace safe/distinct and unchanged. Copies of data in your own account do not consume extra quota space.

STAR normally cannot work with GFF3 data but in Galaxy it can. But should you have problems, try converting to GTF.

You can do all of the data prep within Galaxy once the files are uploaded. FAQ: