1. A method of estimating the number of target polynucleotides in a sample, comprising: ligating a discriminatory oligonucleotide tag to a complex nucleic acid sample comprising multiple molecular species so that substantially every target polynucleotide receives a tag that comprises a unique nucleotide sequence, to produce a tagged sample; amplifying the target polynucleotides in said tagged sample; and determining the number of different tags that are present in the amplified target polynucleotides, thereby providing an estimate of the number of target polynucleotides that are amplified.
1. A method of estimating the number of target polynucleotides in a sample, comprising: ligating a discriminatory oligonucleotide tag to a complex nucleic acid sample comprising multiple molecular species so that substantially every target polynucleotide receives a tag that comprises a unique nucleotide sequence, to produce a tagged sample; amplifying the target polynucleotides in said tagged sample; and determining the number of different tags that are present in the amplified target polynucleotides, thereby providing an estimate of the number of target polynucleotides that are amplified. 6. The method of claim 1 , further comprising sequencing the amplified target polynucleotides.