Annotating Cufflinks Data

[antifolate]

The Cufflinks workflow produces differential expression information from an RNA-Seq data set, but it doesn't include the name of the transcripts in the output GTF files. That's normal because Cufflinks doesn't really have this information.

I'm looking for a way to include the names- and preferrably the functions- of the transcripts in the GTF file produced by Cufflinks, using a genome annotation GTF file. This should be possible since the file includes the coordinates of the transcripts. Does anyone know how to do this?

Thanks.