What’s the Answer? (what is a canonical transcript in UCSC?)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

What is the rationale behind UCSC canonical transcripts?

Several good answers. The short of it is “The canonical transcript is defined as either the longest CDS, if the gene has translated transcripts, or the longest cDNA.” from the UCSC mailing list.

If you want to retrieve the canonical transcripts, you can check out our tip from a little over a year ago, still valid :D.