Re: [galaxy-user] Cuffdiff Question
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-cuf...
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.