I am analyzing my RNA-seq data of Borrelia burgdorferi samples with Galaxy, but when I use RNA Star to map the read to the genome, there is no built-in genome to use, I have downloaded one (.gtf) from NCBI, and uploaded in Galaxy, but there is always some issue, anyone know how to do it, thank you very much!
Have you checked Custom Genomes - Galaxy Community Hub ? RNA Star works with custom genomes but you need to have them in the fasta format.