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
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