Quick question about Cuffdiff assembly option

Question

[--panda--]

Is there any way to forbid transcript assembly and only use the annotation file in cuffdiff/cufflinks? It seems that the software automatically do the assembly even if you feed it with your annotation file.

Answer 1

[Jeffin Rockey]

If you use -G option for cufflinks, the estimation(fpkm tracking files) would be based on the genes and transcripts from the given gtf only.

Similarly in cuffdiff you may provide your GTF in command line prior to the the bam files to have the comparison based on the gtf.