> 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: http://main.g2.bx.psu.edu/u/jeremy/w/make-ensembl-gtf-compatible-with-cufflinks 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. Best, J. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
