Question: Re: Running Cufflinks On A Genome Without A Bowtie Index
6.9 years ago by
Jeremy Goecks • 2.2k
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.
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