A method for the controlled identification and/or quantification of transcript variants in one or more samples, comprising: a) providing a reference set of artificial nucleic acid molecules simulating transcript variants, comprising at least two different families of NA molecules, with each family consisting of at least two different NA molecules, wherein, independently for each family, all NA molecules of said each family are reference transcript variants of the same artificial gene, the gene having at least a transcription start site, a transcribed region and a transcription end site, wherein the reference transcript variants share exons or parts thereof between them that are transcribed from the gene, and wherein, independently for each family, the NA molecules of said each family share a sequence of at least 80 nucleotides (nt) in length and at least two NA molecules of said each family differ by at least another sequence of at least 80 nt length, and wherein at least two of said NA molecules are present in preset molar amounts; and b) adding said reference set as external control to the one or more samples comprising transcript variants; and c1) performing NA sequencing based on read generation and assignment wherein a reference read assignment is generated with the reads of the reference set and said reference read assignment is used to control, verify, or modify the read assignment of the transcript variants of the one or more samples; or c2) performing a NA detection or quantification method, preferably micro-array analysis or qPCR, on the one or more samples, wherein at least one probe binds to at least one NA molecule of the reference set and a measuring result based on a signal resulting from the at least one probe binding to the at least one NA molecule of the reference set is used to control, verify, or modify a measuring result based on a signal resulting from the transcript variants of the one or more samples binding to a probe in said NA detection or quantification method. a) providing a reference set of artificial nucleic acid molecules simulating transcript variants, comprising at least two different families of NA molecules, with each family consisting of at least two different NA molecules, wherein, independently for each family, all NA molecules of said each family are reference transcript variants of the same artificial gene, the gene having at least a transcription start site, a transcribed region and a transcription end site, wherein the reference transcript variants share exons or parts thereof between them that are transcribed from the gene, and wherein, independently for each family, the NA molecules of said each family share a sequence of at least 80 nucleotides (nt) in length and at least two NA molecules of said each family differ by at least another sequence of at least 80 nt length, and wherein at least two of said NA molecules are present in preset molar amounts; and b) adding said reference set as external control to the one or more samples comprising transcript variants; and c1) performing NA sequencing based on read generation and assignment wherein a reference read assignment is generated with the reads of the reference set and said reference read assignment is used to control, verify, or modify the read assignment of the transcript variants of the one or more samples; or c2) performing a NA detection or quantification method, preferably micro-array analysis or qPCR, on the one or more samples, wherein at least one probe binds to at least one NA molecule of the reference set and a measuring result based on a signal resulting from the at least one probe binding to the at least one NA molecule of the reference set is used to control, verify, or modify a measuring result based on a signal resulting from the transcript variants of the one or more samples binding to a probe in said NA detection or quantification method.