Method for generating a labelled nucleic acid from an RNA comprising a 5' protecting group, preferably said protecting group being a 5' cap or a 5' polyphosphate, said method comprises the steps of: a) obtaining a mixture of template strands of nucleic acids, said mixture comprising said RNA and further potentially other nucleic acids without a 5' protecting group, b1) annealing at least one oligonucleotide primer to the RNA template strand and potentially other nucleic acids, and template sequence dependent extending said primer, thereby obtaining a complementary nucleic acid strand annealed to its template strand as duplex, or b2) providing the RNA in duplex with a complementary nucleic acid strand annealed to its template strand, and c) modifying the duplex of said nucleic acids without 5' protecting group and subsequently d1) labelling a complementary nucleic acid of a double stranded nucleic acid, wherein modifying comprises modifying the duplex of said nucleic acids without 5' protecting group either on the 5' end of the template strand or on the 3' end of the complementary strand, or both, wherein the modification removes structures that are selected for during labelling of the duplex nucleic acids with the templates without the 5' protecting group in step d1) and, labelling comprises labelling a complementary nucleic acid of a double stranded nucleic acid not modified in step c), wherein therefore the labelled nucleic acid did have a 5' protecting group on the RNA template strand in step c), said 5' protecting group being optionally removed after performing step c), thereby specifically generating a labelled nucleic acid complementary to an RNA at least originally comprising a 5' protecting group. a) obtaining a mixture of template strands of nucleic acids, said mixture comprising said RNA and further potentially other nucleic acids without a 5' protecting group, b1) annealing at least one oligonucleotide primer to the RNA template strand and potentially other nucleic acids, and template sequence dependent extending said primer, thereby obtaining a complementary nucleic acid strand annealed to its template strand as duplex, or b2) providing the RNA in duplex with a complementary nucleic acid strand annealed to its template strand, and c) modifying the duplex of said nucleic acids without 5' protecting group and subsequently d1) labelling a complementary nucleic acid of a double stranded nucleic acid, wherein modifying comprises modifying the duplex of said nucleic acids without 5' protecting group either on the 5' end of the template strand or on the 3' end of the complementary strand, or both, wherein the modification removes structures that are selected for during labelling of the duplex nucleic acids with the templates without the 5' protecting group in step d1) and, labelling comprises labelling a complementary nucleic acid of a double stranded nucleic acid not modified in step c), wherein therefore the labelled nucleic acid did have a 5' protecting group on the RNA template strand in step c), said 5' protecting group being optionally removed after performing step c), thereby specifically generating a labelled nucleic acid complementary to an RNA at least originally comprising a 5' protecting group.