MOLECULAR LABEL COUNTING ADJUSTMENT METHODS
First Claim
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1. A method for determining the numbers 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 molecular label;
(b) obtaining sequencing data of the stochastically barcoded targets; and
(c) for one or more of the plurality of targets;
(i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data;
(ii) identifying clusters of molecular labels of the target using directional adjacency;
(iii) collapsing the sequencing data obtained in (b) using the clusters of molecular labels of the target identified in (ii); and
(iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) after collapsing the sequencing data in (ii).
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Abstract
Disclosed herein are methods and systems for determining the numbers of targets. In some embodiments, the method comprise: stochastically barcoding targets using stochastic barcodes; obtaining sequencing data; for one or more of the targets: counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; identifying clusters of molecular labels of the target using directional adjacency; collapsing the sequencing data using the clusters of molecular labels of the target identified; and estimating the number of the target.
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Citations
112 Claims
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1. A method for determining the numbers of targets, comprising:
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(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 molecular label; (b) obtaining sequencing data of the stochastically barcoded targets; and (c) for one or more of the plurality of targets; (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) identifying clusters of molecular labels of the target using directional adjacency; (iii) collapsing the sequencing data obtained in (b) using the clusters of molecular labels of the target identified in (ii); and (iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) after collapsing the sequencing data in (ii). - View Dependent Claims (3, 5, 6, 7, 8, 9, 11, 12, 13, 14)
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2. (canceled)
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4. (canceled)
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10. (canceled)
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15. A method for determining the numbers of targets, comprising:
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(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 molecular label; (b) obtaining sequencing data of the stochastically barcoded targets; and (c) for one or more of the plurality of targets; (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) determining a number of noise molecular labels with distinct sequences associated with the target in the sequencing data; and (iii) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) adjusted according to the number of noise molecular labels determined in (ii). - View Dependent Claims (16, 17, 18, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 37)
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19-20. -20. (canceled)
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23. (canceled)
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27. (canceled)
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33. (canceled)
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36. (canceled)
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38-39. -39. (canceled)
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40. A method for determining the numbers of targets, comprising:
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(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 molecular label; (b) obtaining sequencing data of the stochastically barcoded targets; and (c) for one or more of the plurality of targets; (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) determining a quality status of the target in the sequencing data obtained in (b); (iii) determining one or more sequencing data errors in the sequencing data obtained in (b), wherein determining the one or more sequencing data errors in the sequencing data comprises determining one or more of;
the number of the molecular labels with distinct sequences associated with the target in the sequencing data, the quality status of the target in the sequencing data, and the number of molecular labels with distinct sequences in the plurality of stochastic barcodes; and(iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) adjusted according to the one or more sequencing data errors determined in (iii).
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41-110. -110. (canceled)
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111. A method for determining the numbers of targets, comprising:
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(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 molecular label; (b) obtaining sequencing data of the stochastically barcoded targets; and (c) for one or more of the plurality of targets; (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) identifying clusters of molecular labels of the target using directional adjacency; (iii) collapsing the sequencing data obtained in (b) using the clusters of molecular labels of the target identified in (ii); and (iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) after collapsing the sequencing data in (ii).
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112-126. -126. (canceled)
Specification