Abstract: The present invention provides a method for determining a quantification of old and new RNA for a gene, the method comprising: obtaining reads from RNA fragments of a sample, wherein the RNA fragments comprise nucleotide substitutions caused by a metabolic marker, determining statistics of nucleotide mismatches in the reads, determining, based on the statistics of nucleotide mismatches, an error rate indicating a rate of nucleotide mismatches in old RNA and a conversion rate indicating a rate of nucleotide mismatches in new RNA, and determining the quantification of old and newly synthesized RNA for the gene based on the error rate, the conversion rate and the statistics for the gene.