A method comprising: (a) forming a plurality of vessels each comprising (i) a single cell from a sample comprising a plurality of cells, (ii) a plurality of molecular barcoded polynucleotides, and (iii) a vessel barcoded polynucleotide; (b) producing: (i) a first complementary polynucleotide that is complementary to a first cell polynucleotide from the single cell, and (ii) a second complementary polynucleotide that is complementary to a second cell polynucleotide from the single cell; (c) attaching: (i) a first molecular barcoded polynucleotide of the plurality of molecular barcoded polynucleotides to the first complementary polynucleotide, and (ii) a second molecular barcoded polynucleotide of the plurality of molecular barcoded polynucleotides to the second complementary polynucleotide, thereby forming a first single cell single-barcoded polynucleotide and a second single cell single-barcoded polynucleotide; and (d) attaching the vessel barcoded polynucleotide, or an amplified product thereof to (i) the first single cell single-barcoded polynucleotide or an amplified product thereof, and (ii) the second single cell single-barcoded polynucleotide or an amplified product thereof, thereby forming a first single cell dual-barcoded sequence and a second single cell dual-barcoded sequence. (a) forming a plurality of vessels each comprising (i) a single cell from a sample comprising a plurality of cells, (ii) a plurality of molecular barcoded polynucleotides, and (iii) a vessel barcoded polynucleotide; (i) a single cell from a sample comprising a plurality of cells, (ii) a plurality of molecular barcoded polynucleotides, and (iii) a vessel barcoded polynucleotide; (b) producing: (i) a first complementary polynucleotide that is complementary to a first cell polynucleotide from the single cell, and (ii) a second complementary polynucleotide that is complementary to a second cell polynucleotide from the single cell; (i) a first complementary polynucleotide that is complementary to a first cell polynucleotide from the single cell, and (ii) a second complementary polynucleotide that is complementary to a second cell polynucleotide from the single cell; (c) attaching: (i) a first molecular barcoded polynucleotide of the plurality of molecular barcoded polynucleotides to the first complementary polynucleotide, and (ii) a second molecular barcoded polynucleotide of the plurality of molecular barcoded polynucleotides to the second complementary polynucleotide, thereby forming a first single cell single-barcoded polynucleotide and a second single cell single-barcoded polynucleotide; and (i) a first molecular barcoded polynucleotide of the plurality of molecular barcoded polynucleotides to the first complementary polynucleotide, and (ii) a second molecular barcoded polynucleotide of the plurality of molecular barcoded polynucleotides to the second complementary polynucleotide, (d) attaching the vessel barcoded polynucleotide, or an amplified product thereof to (i) the first single cell single-barcoded polynucleotide or an amplified product thereof, and (ii) the second single cell single-barcoded polynucleotide or an amplified product thereof, thereby forming a first single cell dual-barcoded sequence and a second single cell dual-barcoded sequence. (i) the first single cell single-barcoded polynucleotide or an amplified product thereof, and (ii) the second single cell single-barcoded polynucleotide or an amplified product thereof, thereby forming a first single cell dual-barcoded sequence and a second single cell dual-barcoded sequence.