I’m starting using cufflinks after the TopHat2 alignment. Looking at the manual I can see that there are several options to add to this tool, but in particular what is not clear to me is if I have to use the trascriptome or the genome as reference. I run the program using this command line
cufflinks -p 4 -N -g Homo_sapiens.GRCh37.75.gtf file.bam -o cuffresults
As you can see, I used the reference genome annotation,is tat correct? I’m also wondering if I can use a trascriptome annotation downloaded from ensemble (Homo_sapiens.GRCh38.cdna.all.fa.gz) or I have to build it from the reference genome ?