Immune receptor-barcode error correction

A method for determining occurrences of targets, comprising:

• (a) stochastically barcoding a plurality of targets using a plurality of stochastic barcodes to create a plurality of stochastically barcoded targets, wherein each of the plurality of stochastic barcodes comprises a cell label and a molecular label, wherein molecular labels of at least two stochastic barcodes of the plurality of stochastic barcodes comprise different molecular label sequences, and wherein at least two stochastic barcodes of the plurality of stochastic barcodes comprise cell labels with an identical cell label sequence;
• (b) obtaining sequencing data of the stochastically barcoded targets;
• and
• (c) for at least one target of the plurality of targets:
• (i) identifying putative sequences of the target in the sequencing data;
• (ii) counting occurrences of molecular label sequences associated with the putative sequences of the target in the sequencing data identified in (i);
• (iii) identifying clusters of the putative sequences of the target;
• (iv) collapsing the sequencing data obtained using the clusters of putative sequences of the target identified in (iii);
• (v) identifying clusters of the molecular label sequences associated with the putative sequences of the target;
• (vi) collapsing the sequencing data using the clusters of molecular label sequences identified in (v);
• (vii) identifying clusters of combination sequences, wherein each combination sequence comprises a sequence of the sequences of the target and an associated molecular label sequence of the molecular label sequences;
• (viii) collapsing the sequencing data using the clusters of combination sequences identified in (vii);
• (ix) identifying one or more putative sequences of the target that correspond to one or more chimeric sequences of the target, wherein occurrences of the one or more putative sequences of the target that correspond to the one or more chimeric sequences of the target are smaller than occurrences of remaining one or more putative sequences of the target that do not correspond to the one or more chimeric sequences of the target;
• (x) removing the one or more putative sequences of the target corresponding to the one or more chimeric sequences of the target identified in (ix) from the sequencing data;
• and
• (xi) estimating the occurrence of the target, wherein the occurrence of the target estimated correlates with the number of molecular label sequences counted in (ii) after collapsing the sequencing data in (iv), (vi), and (viii) and removing the one or more putative sequences of the target that correspond to the one or more chimeric sequences of the target in (x).