I am trying to use Cuffdiff to analyze differential expression between two experimental groups. I used cufflinks and cuffmerge to produce the gtf assembly. When I run cuffdiff though I keep on getting empty output files. No error message comes up either.
This is the command I am running:
cuffdiff path_to_gtf path_to_data1 path_to_data2
How should I modify this command to get this to run properly?
I am only using one file for each sample group until I get the program to work. How do I incorporate the rest of the files as well?
The gene annotation file used in Cuffmerge has the p_id and tss_id. Do i have to include the gene annotation file in Cufflinks as well (as opposed to only cuffmerge)?