The present invention includes, but is not limited to, methods, assays, and compositions for preparing libraries of nucleic acid molecules from biological samples, and for detecting and measuring the abundances of nucleic acid molecules, including RNA and DNA. The methods, assays, and compositions of the present invention provide in whole or in part for the detecting and measuring the abundances of nucleic acid molecules, and particularly but not limited to those nucleic acids that have structures that cannot be determined reliably by routine alignment to a reference sequence or concatenation of smaller sequences by matching homologous ends.