This focus presents the results of the RNA Sequencing Quality Control (SEQC) project of the MicroArray Quality Control (MAQC) Consortium that sought to evaluate the comparability of RNA-seq data from many different laboratories and of assessing different sequencing platforms and data analysis approaches and their performance compared with DNA microarrays. Ultimately, these multi-platform, cross-site studies will enable RNA-seq to be applied more broadly in analyzing large cohorts for discovery research and clinical use.