Question: Re: Running Cufflinks On A Genome Without A Bowtie Index
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Jeremy Goecks • 2.2k wrote:
Noa,
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.
Good luck,
J.