Weimin Zhao, It's not possible to use Trinity output directly with Cuffcompare. You'll need to map your Trinity transcripts back to your reference genome using something like Blat or Lastz, convert the mapped transcripts to GTF format, and then run Cuffcompare. You can run Lastz in Galaxy, but it's not clear to me how to convert Lastz's output to GTF format, especially the format required by Cuffcompare. You might try emailing the Cufflinks' authors directly or the Trinity mailing list for some ideas. Good luck, J. On Sep 26, 2011, at 11:08 AM, dongdong zhaoweiming wrote:

hi, I want to use Cuffcompare to compare my assembled transcripts to a reference annotation. My assembled transcripts is a Fasta format produced by trinity, but Cuffcompare requried GTF file , so what should I do? Thank you! weimin zhao ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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