I am using cufflinks in Galaxy, but I faced with the problem with FPKMs.
When I use gtf file (hg19: shared data > data libraries > iGenomes )and reference genome for human available in Galaxy(hg19: a tophat option), the cufflinks output gives me genes ID, but most FPKMs are zero.
Can you help me find out the problem?
How can I choose a compatible reference genome for that GTF file?
Thank you in advance