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Bookend: precise transcript reconstruction with end-guided assembly
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DOI：10.1186/s13059-022-02700-3.png)
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摘要
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We developed Bookend, a package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5' and 3' ends. We demonstrate that correct identification of transcript start and end sites is essential for precise full-length transcript assembly. Utilization of end-labeled reads present in full-length single-cell RNA-seq datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis thaliana, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells, can produce reference-quality end-to-end transcript annotations.
Keyword:
RNA-seq
Transcriptome
Single-cell
TSS
PAS
Capping
Polyadenylation
5 ' and 3 ' ends
Long-read
Iso-Seq
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