Members of the Animal Genome to Phenome Research Coordination Network discussed best practices for the de novo assembly, annotation, and expression analysis of RNA-seq data. The AG2P RCN collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Discussion participants studied a great variety of organisms, and represented laboratories present in both the US and abroad (see above figure). A policy paper summarizing community needs, computational pipelines, current resources and future directions has recently been published in Integrative and Comparative Biology.