scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data
Abstract The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3′ scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method, scTail, to identify PAS using first-strand reads...
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| Format: | Article |
| Language: | English |
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BMC
2025-08-01
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| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-025-03710-7 |
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| author | Ruiyan Hou Yuanhua Huang |
| author_facet | Ruiyan Hou Yuanhua Huang |
| author_sort | Ruiyan Hou |
| collection | DOAJ |
| description | Abstract The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3′ scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method, scTail, to identify PAS using first-strand reads and quantify its expression leveraging second-strand reads, consequently enabling detection of alternative PAS usage. Compared with other methods, scTail detects PAS more precisely and retains high sensitivity. Furthermore, we demonstrated that combining scTail and BRIE2 can discover differential alternative PAS usage in various biological processes including cancers and time-series development, giving critical insight into PAS regulation. |
| format | Article |
| id | doaj-art-77b24ff85c854af7a4561c0c68477280 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-77b24ff85c854af7a4561c0c684772802025-08-20T04:02:54ZengBMCGenome Biology1474-760X2025-08-0126112510.1186/s13059-025-03710-7scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq dataRuiyan Hou0Yuanhua Huang1School of Biomedical Sciences, University of Hong KongSchool of Biomedical Sciences, University of Hong KongAbstract The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3′ scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method, scTail, to identify PAS using first-strand reads and quantify its expression leveraging second-strand reads, consequently enabling detection of alternative PAS usage. Compared with other methods, scTail detects PAS more precisely and retains high sensitivity. Furthermore, we demonstrated that combining scTail and BRIE2 can discover differential alternative PAS usage in various biological processes including cancers and time-series development, giving critical insight into PAS regulation.https://doi.org/10.1186/s13059-025-03710-7 |
| spellingShingle | Ruiyan Hou Yuanhua Huang scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data Genome Biology |
| title | scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data |
| title_full | scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data |
| title_fullStr | scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data |
| title_full_unstemmed | scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data |
| title_short | scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data |
| title_sort | sctail precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3 scrna seq data |
| url | https://doi.org/10.1186/s13059-025-03710-7 |
| work_keys_str_mv | AT ruiyanhou sctailprecisepolyadenylationsitedetectionanditsalternativeusageanalysisfromreads1preserved3scrnaseqdata AT yuanhuahuang sctailprecisepolyadenylationsitedetectionanditsalternativeusageanalysisfromreads1preserved3scrnaseqdata |