Thanks for the reply. I tried to use the script provided on a previous galaxy thread for adding the chr on to the gtf file on the mac terminal but I keep getting this error -
awk: can't open file ensembl.gtf source line number 1
I am very new to using the terminal so please let me know if there is something basic that I am not doing right,
Try this Galaxy workflow:
It simply prepends 'chr' to the chromosome name, which is needed if you're using an Ensemble reference annotation and want to use it with Cufflinks/compare/diff in Galaxy.