> 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.

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