4.3 years ago by
If you mean that you have constructed multiple annotated transcriptomes (assemblies of sorts), and wish to compare, then this can be done many ways. The tools in the groups Extract Features, Operate on Genomic Intervals, and BEDTools should get you started. Seach by your datatype to locate all tools available for each - the description and help will aid you in knowing what operation is performed. And of course comparing to any known annotation will be helpful.
In the end, actually taking a look at the data would be a good idea. Visualizing in a browser both together (perhaps examine a gene bound that has been characterized) and along with other annotation types and maybe some of the comparison datasets. All of these choices may not be available for all genomes, but are for many, and there are techniques to map annotation (RefSeq, Ensemble) across species, to aid in gene bound/transcript elucidation (BLAT, Blast+, etc - can be used in a local/cloud Galaxy).
Perhaps our community will also contribute more ideas. I'll assumed you have already reviewed available advice on http://biostars.org, http://seqanswers.com, etc, .. but if not, these are great resources.
Good luck, and if your question has been misunderstood, please provide more details.