Using your FASTA in Tophat and Cufflinks is the correct approach. You don't need to provide an annotation file in Cufflinks, and you can also avoid using your FASTA in Cufflinks by not using bias correction.

If you're still having problems, the issue is likely your parameter choices in Tophat and/or Cufflinks. You'll want to read the documentation carefully to choose parameters appropriately for your data.

On Dec 22, 2011, at 5:09 AM, Noa Sher wrote:

Hi
I am trying to run Cufflinks on a genome without a bowtie index.
How do I make my own index? I have a FASTA file of the genome, but if I run tophat using just that and then cufflinks using a gtf file of the transcriptome, I get zero in all FPKM values
Thanks
Noa
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