A method of assigning sequencing data to partitions, comprising: providing a plurality of partitions each comprising a plurality of partition indexing oligonucleotides, wherein the partition indexing oligonucleotides each comprises a predetermined partition indexing sequence, wherein partition indexing oligonucleotides situated within the same partition comprise the same partition indexing sequence, and wherein partition indexing oligonucleotides situated within different partitions comprise different partition indexing sequences; partitioning a plurality of solid supports and a plurality of single cells to the plurality of partitions, wherein the single cells each comprises copies of a nucleic acid target, wherein the plurality of solid supports each comprises a plurality of oligonucleotide barcodes each comprising a cell label sequence, wherein oligonucleotide barcodes associated with the same solid support comprise the same cell label sequence, and wherein oligonucleotide barcodes associated with different solid supports comprise different cell label sequences; barcoding the partition indexing oligonucleotides using the plurality of oligonucleotide barcodes to generate a plurality of barcoded partition indexing oligonucleotides; barcoding the copies of a nucleic acid target from at least one of the plurality of single cells using the plurality of oligonucleotide barcodes to generate a plurality of barcoded nucleic acid targets; obtaining sequencing data comprising a plurality of sequencing reads of the barcoded partition indexing oligonucleotides, or products thereof, and the plurality of barcoded nucleic acid targets, or products thereof; identifying the partition indexing sequence associated with each cell label sequence in the sequencing data; and assigning each of the plurality of sequencing reads to a partition of the plurality of partitions based on the partitioning indexing sequence associated with each cell label sequence in the sequencing data. providing a plurality of partitions each comprising a plurality of partition indexing oligonucleotides, wherein the partition indexing oligonucleotides each comprises a predetermined partition indexing sequence, wherein partition indexing oligonucleotides situated within the same partition comprise the same partition indexing sequence, and wherein partition indexing oligonucleotides situated within different partitions comprise different partition indexing sequences; partitioning a plurality of solid supports and a plurality of single cells to the plurality of partitions, wherein the single cells each comprises copies of a nucleic acid target, wherein the plurality of solid supports each comprises a plurality of oligonucleotide barcodes each comprising a cell label sequence, wherein oligonucleotide barcodes associated with the same solid support comprise the same cell label sequence, and wherein oligonucleotide barcodes associated with different solid supports comprise different cell label sequences; barcoding the partition indexing oligonucleotides using the plurality of oligonucleotide barcodes to generate a plurality of barcoded partition indexing oligonucleotides; barcoding the copies of a nucleic acid target from at least one of the plurality of single cells using the plurality of oligonucleotide barcodes to generate a plurality of barcoded nucleic acid targets; obtaining sequencing data comprising a plurality of sequencing reads of the barcoded partition indexing oligonucleotides, or products thereof, and the plurality of barcoded nucleic acid targets, or products thereof; identifying the partition indexing sequence associated with each cell label sequence in the sequencing data; and assigning each of the plurality of sequencing reads to a partition of the plurality of partitions based on the partitioning indexing sequence associated with each cell label sequence in the sequencing data. <EOS>