<p>I performed denovo assembly with Trinity using reads from heart mouse RNaseq. Than I mapped the transcriptome back to the reference genome with Blat . I also used Kallisto to Count the transcript abbundance in each sample. But now I want to know what Trinity ID&#39;s are known already in the annotation and what their names, and what is not annotated. How can I do that?</p>

**Now, for a correct answer**.

You are doing mice which is a really well annotated organism. Trinity will be imprecise. You would be way better using Cufflinks with the reference genome and annotation, if you are looking for novel isoforms or things like that it will find them for you. Are trying to achieve something in particular?

Cufflinks will also give you the correspondence between its gene names and the official ones.