Fig. 1.

Typical decision lines in coding and non-coding transcript assembly. The upper part summarizes wet experimental procedures required to produce RNA-Seq reads. The lower part highlights the computational analyses and decision lines. Transcript assembly starts with the evaluation of read quality, and can proceed with or without reference annotations. Blue square boxes denote decision points on tools to use, and arrows denote strategic considerations in how to analyze the RNA-Seq data. Dotted lines indicate optional pathways. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)