I am a beginner in RNAseq Galaxy interface and I have a problem with all zero FPKM values in cuffdiff output. I used SusScr3 build in genome for tophat alignment and SusScrofa 10.2.gtf from UCSC for cuffdiff. How can I check if these two files are compatible? Where I can download gtf.file compatible to SusScr3 build in genome?
Thank you for all answers