Using cuffdiff for isoform DE

[Xinlitik]

After running CuffDiff on my two conditions, I have the differential expression for various isoforms of genes in isoforms_exp. I would like to determine which isoforms are actually involved (ie the sequence of the alternate transcript) but I can't figure out how to get that information. The only identifying difference I can see between isoforms is the internal ID used by cufflinks, so it seems like that would be the key, but I don't know how to translate the internal ID into useful information in a genome browser, for instance.

Does anyone know how this can be done? Thanks

[tlifeyu]

Cuffcompare may be used compare with reference annotation.