Analysis 
Here's the start point of a series of in silico analysis steps dedicated to obtain in fine transcript identifications from your RFDD experimental results.
You can find an overview of the analysis process here.
Depending of what you already did, you can start at different points :
Alignment
If you never did an analysis of your RFDD experimental results, start to read this help page. Then click on "Start Alignment" and follow step by step the analysis process.
You can test it with one those data set.
Identification
If you already did a previous analysis you may have the .rfdd file containing alignment results. Then you can re-identify the corresponding transcripts with an updated RFDB database.
Covariation
If you have the results of several comparable RFDD experiments, you can extract the list of all transcripts that behave in the same way.
Start Covariation
