I am trying to use cuffnorm to normalise the counts. However, I am giving inputs as BAM files and I have the GTF obtained from ensembl. Do I need to use cufflinks as the first step to generate the GTF to be used with Cuffnorm or can I use the GTF that I have obtained from emnsebl for the genome to which I aligned the data?
I would be grateful for your advise?
Thank you Yaseen