A method for analyzing cells, comprising: (a) (i) labeling a first cell with a first cell nucleic acid barcode sequence to generate a first labeled cell, wherein a first cell nucleic acid barcode molecule comprises said first cell nucleic acid barcode sequence and a lipophilic moiety; (ii) labeling a second cell with a second cell nucleic acid barcode sequence to generate a second labeled cell, wherein a second nucleic acid barcode molecule comprises said second cell nucleic acid barcode sequence and a cell binding moiety; (b) generating (i) a first partition comprising said first labeled cell and a plurality of first partition nucleic acid barcode molecules which comprise a first partition nucleic acid barcode sequence; and (ii) a second partition comprising said second labeled cell and a plurality of second partition nucleic acid barcode molecules which comprise a second partition nucleic acid barcode sequence; (c) permeabilizing or lysing said first and second cells to provide access to a plurality of nucleic acid molecules therein; (d) in said first partition, generating (i) a first barcoded nucleic acid molecule comprising said first cell nucleic acid barcode sequence or a complement thereof, and said first partition nucleic acid barcode sequence or a complement thereof; and (ii) a plurality of barcoded nucleic acid products each comprising a sequence of a nucleic acid molecule of said plurality of nucleic acid molecules from said first cell and said first partition nucleic acid barcode sequence or a complement thereof; (e) in said second partition, generating (i) a second barcoded nucleic acid molecule comprising said second cell nucleic acid barcode sequence or a complement thereof, and said second partition nucleic acid barcode sequence or a complement thereof; and (ii) a plurality of barcoded nucleic acid products each comprising a sequence of a nucleic acid molecule of said plurality of nucleic acid molecules from said second cell and said second partition nucleic acid barcode sequence or a complement thereof; and (f) identifying said plurality of nucleic acid molecules as originating from said first and second cells. (a) (i) labeling a first cell with a first cell nucleic acid barcode sequence to generate a first labeled cell, wherein a first cell nucleic acid barcode molecule comprises said first cell nucleic acid barcode sequence and a lipophilic moiety; (ii) labeling a second cell with a second cell nucleic acid barcode sequence to generate a second labeled cell, wherein a second nucleic acid barcode molecule comprises said second cell nucleic acid barcode sequence and a cell binding moiety; (i) labeling a first cell with a first cell nucleic acid barcode sequence to generate a first labeled cell, wherein a first cell nucleic acid barcode molecule comprises said first cell nucleic acid barcode sequence and a lipophilic moiety; (ii) labeling a second cell with a second cell nucleic acid barcode sequence to generate a second labeled cell, wherein a second nucleic acid barcode molecule comprises said second cell nucleic acid barcode sequence and a cell binding moiety; (b) generating (i) a first partition comprising said first labeled cell and a plurality of first partition nucleic acid barcode molecules which comprise a first partition nucleic acid barcode sequence; and (ii) a second partition comprising said second labeled cell and a plurality of second partition nucleic acid barcode molecules which comprise a second partition nucleic acid barcode sequence; (i) a first partition comprising said first labeled cell and a plurality of first partition nucleic acid barcode molecules which comprise a first partition nucleic acid barcode sequence; and (ii) a second partition comprising said second labeled cell and a plurality of second partition nucleic acid barcode molecules which comprise a second partition nucleic acid barcode sequence; (c) permeabilizing or lysing said first and second cells to provide access to a plurality of nucleic acid molecules therein; (d) in said first partition, generating (i) a first barcoded nucleic acid molecule comprising said first cell nucleic acid barcode sequence or a complement thereof, and said first partition nucleic acid barcode sequence or a complement thereof; and (ii) a plurality of barcoded nucleic acid products each comprising a sequence of a nucleic acid molecule of said plurality of nucleic acid molecules from said first cell and said first partition nucleic acid barcode sequence or a complement thereof; (e) in said second partition, generating (i) a second barcoded nucleic acid molecule comprising said second cell nucleic acid barcode sequence or a complement thereof, and said second partition nucleic acid barcode sequence or a complement thereof; and (ii) a plurality of barcoded nucleic acid products each comprising a sequence of a nucleic acid molecule of said plurality of nucleic acid molecules from said second cell and said second partition nucleic acid barcode sequence or a complement thereof; and (i) a second barcoded nucleic acid molecule comprising said second cell nucleic acid barcode sequence or a complement thereof, and said second partition nucleic acid barcode sequence or a complement thereof; and (ii) a plurality of barcoded nucleic acid products each comprising a sequence of a nucleic acid molecule of said plurality of nucleic acid molecules from said second cell and said second partition nucleic acid barcode sequence or a complement thereof; and (f) identifying said plurality of nucleic acid molecules as originating from said first and second cells.