ArticleGenome biology2022
Bookend: precise transcript reconstruction with end-guided assembly.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
8 citing papers in PubMed.
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Anchorage accurately assembles anchor-flanked synthetic long reads.Algorithms for molecular biology : AMB · 2025Article
- Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2024Article
- Merging short and stranded long reads improves transcript assembly.PLoS computational biology · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Publisher Correction: Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter.International journal of molecular sciences · 2022Review
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.