I have attached the file, any help would be great.
Here's the first line in the file: -- Mito intergenic_50 exon 1 680 . + . gene_id "INT50_3749" ; transcript_name "INT50_3749"; transcript_id "INT50_3749"; gene_name "INT50_3749" ; Note "intergenic regions 50 nt from a coding sequence" -- As it turns out, the file is not technically a GTF file. The GTF spec is here: http://genome.ucsc.edu/FAQ/FAQformat#format4 and the requirement broken by this file is: -- The attribute list must begin with the two mandatory attributes: • gene_id value - A globally unique identifier for the genomic source of the sequence. • transcript_id value - A globally unique identifier for the predicted transcript. -- Where did you get this file? If there are prominent tools that are producing almost-but-not-quite-compliant GTF files, it may be necessary for Galaxy to relax its requirements a bit. Thanks, J.