Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers
Abstract Single-cell RNA-seq (scRNA-seq) profiles gene expression of individual cells. Unique molecular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain reaction, a major source of noise. For scRNA-seq data lacking UMIs, we propose quasi-UMIs: quantile normalizatio...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2020-07-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02078-0 |
| _version_ | 1818081338146684928 |
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| author | F. William Townes Rafael A. Irizarry |
| author_facet | F. William Townes Rafael A. Irizarry |
| author_sort | F. William Townes |
| collection | DOAJ |
| description | Abstract Single-cell RNA-seq (scRNA-seq) profiles gene expression of individual cells. Unique molecular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain reaction, a major source of noise. For scRNA-seq data lacking UMIs, we propose quasi-UMIs: quantile normalization of read counts to a compound Poisson distribution empirically derived from UMI datasets. When applied to ground-truth datasets having both reads and UMIs, quasi-UMI normalization has higher accuracy than competing methods. Using quasi-UMIs enables methods designed specifically for UMI data to be applied to non-UMI scRNA-seq datasets. |
| first_indexed | 2024-12-10T19:04:37Z |
| format | Article |
| id | doaj.art-c5ee6248f531484f814b7cfaa0e26db4 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-10T19:04:37Z |
| publishDate | 2020-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-c5ee6248f531484f814b7cfaa0e26db42022-12-22T01:36:56ZengBMCGenome Biology1474-760X2020-07-0121111710.1186/s13059-020-02078-0Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiersF. William Townes0Rafael A. Irizarry1Department of Computer Science, Princeton UniversityDepartment of Data Sciences, Dana-Farber Cancer InstituteAbstract Single-cell RNA-seq (scRNA-seq) profiles gene expression of individual cells. Unique molecular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain reaction, a major source of noise. For scRNA-seq data lacking UMIs, we propose quasi-UMIs: quantile normalization of read counts to a compound Poisson distribution empirically derived from UMI datasets. When applied to ground-truth datasets having both reads and UMIs, quasi-UMI normalization has higher accuracy than competing methods. Using quasi-UMIs enables methods designed specifically for UMI data to be applied to non-UMI scRNA-seq datasets.http://link.springer.com/article/10.1186/s13059-020-02078-0Gene expressionSingle cellRNA-seqNormalizationQuasi-UMI |
| spellingShingle | F. William Townes Rafael A. Irizarry Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers Genome Biology Gene expression Single cell RNA-seq Normalization Quasi-UMI |
| title | Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers |
| title_full | Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers |
| title_fullStr | Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers |
| title_full_unstemmed | Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers |
| title_short | Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers |
| title_sort | quantile normalization of single cell rna seq read counts without unique molecular identifiers |
| topic | Gene expression Single cell RNA-seq Normalization Quasi-UMI |
| url | http://link.springer.com/article/10.1186/s13059-020-02078-0 |
| work_keys_str_mv | AT fwilliamtownes quantilenormalizationofsinglecellrnaseqreadcountswithoutuniquemolecularidentifiers AT rafaelairizarry quantilenormalizationofsinglecellrnaseqreadcountswithoutuniquemolecularidentifiers |