A method for detecting chimeric artefact polynucleotides produced during amplification of a mixed sample of RNA molecules, the method comprising: (i) capturing RNA molecules of the sample on a set of capture polynucleotides, wherein the capture polynucleotides each comprise a sample RNA capture region, one of a mixed pool of first identifier sequences, and a PCR handle sequence; (ii) performing reverse transcription of captured sample RNA molecules using a template switch reverse polymerase and primed using the capture polynucleotides to generate cDNA polynucleotides having 3' end non-templated nucleotides; (iii) annealing a set of template switch oligonucleotides (TSOs) to the 3' end non-templated nucleotides, wherein the TSOs each comprise one of a mixed pool of second identifier sequences, wherein the first identifier sequences and/or the second identifier sequences each comprise a series of discrete nucleotide blocks, wherein the discrete nucleotide blocks are from a mixed pool of nucleotide blocks of known sequence, and wherein each nucleotide block sequence in the pool differs from each other nucleotide block in the pool by at least two nucleotide substitutions; (iv) amplifying the cDNA using the capture polynucleotide PCR handle sequences and TSO PCR handle sequences to generate a library of amplified cDNA flanked by first and second identifier sequences; (v) sequencing the library; (vi) identifying pairings of first and second identifier sequences flanking the library cDNA molecules; (vii) counting library cDNA molecules having identified pairings of first and second identifier sequences and identifying pairings that are under-represented in the library; and/or identifying pairings as mismatch pairings when they comprise a. a first identifier sequence in common with another pairing in the library having a different second identifier sequence to the mismatch pairing; and/or b. a second identifier sequence in common with another pairing in the library having a different first identifier sequence to the mismatch pairing; and (viii) identifying a library cDNA molecule that is: a. flanked by an underrepresented pairing of first and second identifier sequences; and/or b. flanked by a mismatch pairing of first and second identifier sequences; as a chimeric artefact polynucleotide. (i) capturing RNA molecules of the sample on a set of capture polynucleotides, wherein the capture polynucleotides each comprise a sample RNA capture region, one of a mixed pool of first identifier sequences, and a PCR handle sequence; (ii) performing reverse transcription of captured sample RNA molecules using a template switch reverse polymerase and primed using the capture polynucleotides to generate cDNA polynucleotides having 3' end non-templated nucleotides; (iii) annealing a set of template switch oligonucleotides (TSOs) to the 3' end non-templated nucleotides, wherein the TSOs each comprise one of a mixed pool of second identifier sequences, wherein the first identifier sequences and/or the second identifier sequences each comprise a series of discrete nucleotide blocks, wherein the discrete nucleotide blocks are from a mixed pool of nucleotide blocks of known sequence, and wherein each nucleotide block sequence in the pool differs from each other nucleotide block in the pool by at least two nucleotide substitutions; (iv) amplifying the cDNA using the capture polynucleotide PCR handle sequences and TSO PCR handle sequences to generate a library of amplified cDNA flanked by first and second identifier sequences; (v) sequencing the library; (vi) identifying pairings of first and second identifier sequences flanking the library cDNA molecules; (vii) counting library cDNA molecules having identified pairings of first and second identifier sequences and identifying pairings that are under-represented in the library; and/or identifying pairings as mismatch pairings when they comprise a. a first identifier sequence in common with another pairing in the library having a different second identifier sequence to the mismatch pairing; and/or b. a second identifier sequence in common with another pairing in the library having a different first identifier sequence to the mismatch pairing; and a. a first identifier sequence in common with another pairing in the library having a different second identifier sequence to the mismatch pairing; and/or b. a second identifier sequence in common with another pairing in the library having a different first identifier sequence to the mismatch pairing; and (viii) identifying a library cDNA molecule that is: a. flanked by an underrepresented pairing of first and second identifier sequences; and/or b. flanked by a mismatch pairing of first and second identifier sequences; as a chimeric artefact polynucleotide. a. flanked by an underrepresented pairing of first and second identifier sequences; and/or b. flanked by a mismatch pairing of first and second identifier sequences;