I see the parameter of cuffdiff is
cuffdiff transcripts.gtf 1.bam 2.bam
Does this transcritpts.gtf is the output of cufflinks or just the reference transcript annotation?
Thanks
cuffdiff transcripts.gtf 1.bam 2.bam
Does this transcritpts.gtf is the output of cufflinks or just the reference transcript annotation?
Thanks