I’m trying to use the STAR RNAseq aligner with a custom reference genome for the chinese hamster and always run into the error “Fatal INPUT FILE error, no valid exon lines in the GTF file”. I checked the chromosome naming in both the genomic fasta as well as the genomic gtf file (which I have both from Refseq), since this is suggested as potentially solution. Judging from the following the chromosome name is the same in both files and I’m now wondering what the problem could be. I also did the recommended normalization of the fasta file on the galaxy server but that didn’t help unfotunately.
Thanks in advance!