I have RNASeq data obtained from bacterial drug resistant and drug sensitive samples.
I conducted mapping using BWA-MEM in galaxy using the reference genome.
But when I run cuffDiff to obtain the list of differential expressed genes using the gtf file, the value1 and value 2 of all genes are zero and as a result the logFC of all genes are zero too.
Since the mapping step seems to have been performed correctly I suspected to the gtf file that I had used.
The species is Pseudomonas aeruginosa PA14 and I get its genome sequence and gtf file from Pseudomonas genome database.
Can anybody help me to figure out the possible sources of this problem?