re-annotating cuffdiff output?

[beeman]

I have gene_set data from two sources, one from ncbi and one from the honeybee genome consortium (beebase). I performed my cufflinks/cuffmerge/cuffdiff workflow using the ncbi annotations and now I'd like to reannotate the cuffdiff output to see if any of the novel transcripts identified by cufflinks are described in the beebase annotations..

If it possible to just update the transcript id's instead of running cuffmerge/cuffdiff again?

Thanks,

[sdriscoll]

why wouldn't you just use cuffcompare to compare your annotation generated from cuffmerge with the one from beebase?

[beeman]

Thanks for the advice, I'll give that a go.

[sdriscoll]

I should add that the idea only works if both annotations are relative to the same genome.