Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. There are multiple published methods for strand-specific RNA-seq, but no consensus exists as to how to choose between them. Researchers at MIT and the Hebrew University, Jerusalem compared seven library-construction protocols and found marked differences in strand specificity, library complexity, evenness and continuity of coverage, agreement with known annotations and accuracy for expression profiling.
Included in the supplemental materials are some nice tables summarizing the details of each method as well as the advantages and disadvantages of each method.
Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods [Epub ahead of print]. [abstract]