Methods and systems for characterizing nucleic acid molecules

A method for determining an epigenetic state or characteristic of a nucleic acid molecule from a single cell, comprising:

• (a) providing a cell bead comprising said nucleic acid molecule from said single cell, wherein said nucleic acid molecule contains or is suspected of containing one or more epigenetic features;
• (b) partitioning said cell bead with a nucleic acid barcode molecule comprising a cell barcode sequence in a single partition among a plurality of partitions;
• (c) in said partition, using said nucleic acid molecule and said nucleic acid barcode molecule to synthesize a barcoded nucleic acid molecule, which barcoded nucleic acid molecule comprises said cell barcode sequence, wherein said cell barcode sequence is indicative of said single cell from which said nucleic acid molecule originates;
• (d) processing said barcoded nucleic acid molecule or a derivative thereof to identify said one or more epigenetic features and said cell barcode;
• and
• (e) using said one or more epigenetic features and said cell barcode sequence to determine said epigenetic state or characteristic of said nucleic acid molecule as being associated with said single cell,
• wherein, subsequent to (a), one or more reactions selected from the group consisting of oxygenase treatment, enzymatic deamination, proteinase treatment, methyltransferase treatment, treatment with methylation-specific restriction enzyme, micrococcal nuclease (Mnase) digestion, deoxyribonuclease (DNase) digestion, cross-linking treatment, immunoprecipitation, restriction digestion, transposase-mediated fragmentation, and proximity ligation are performed within said cell bead, said one or more reactions transforming at least a portion of said one or more epigenetic features of said nucleic acid molecule.