Genome-guided transcript assembly by integrative analysis of RNA sequence data
Open accessAbstract
The identification of full length transcripts entirely from short-read RNA sequencing data (RNA-seq) remains a challenge in the annotation of genomes. Here we describe an automated pipeline for genome annotation that integrates RNA-seq and gene-boundary data sets, which we call Generalized RNA Integration Tool, or GRIT. Applying GRIT to Drosophila melanogaster short-read RNA-seq, cap analysis of gene expression (CAGE) and poly(A)-site-seq data collected for the modENCODE project, we recovered the vast majority of previously annotated transcripts and doubled the total number of transcripts cataloged. We found that 20% of protein coding genes encode multiple protein-localization signals and that, in 20-d-old adult fly heads, genes with multiple polyadenylation sites are more common than genes with alternative splicing or alternative promoters. GRIT demonstrates 30% higher precision and recall than the most widely used transcript assembly tools. GRIT will facilitate the automated generation of high-quality genome annotations without the need for extensive manual annotation.
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Tools such as GRIT that incorporate other data such as 5' ends from CAGE or RAMPAGE typically have a better chance of annotating the major expressed isoforms correctly.
“In addition, it is difficult to identify transcription start and end sites [21], and tools such as GRIT [22] that incorporate other data such as 5’ ends from CAGE or RAMPAGE typically have a better chance of annotating the major expressed isoforms correctly.”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [22]
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Self-citation
- Authors
- Boley, N., Stoiber, M. H., Booth, B. W., Wan, K. H., Hoskins, R. A., Bickel, P. J., Celniker, S. E., & Brown, J. B.
- Affiliations
- University of California, Berkeley (US)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Boley, Nathan
- Celniker, Susan E
- Venue
- Nature Biotechnology
- Published
- 2014-03-16
- Volume
- 32
- Issue
- 4
- Pages
- 341-346
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC4037530
- OpenAlex
- W2010394934
- Cited by
- 48
- References
- 40
- Citations by year
- 2026: 1 · 2023: 2 · 2022: 1 · 2021: 5 · 2020: 3 · 2019: 4 · 2018: 2 · 2017: 7 · 2016: 6 · 2015: 12 · 2014: 5
- FWCI
- 4.10
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Funders
- National Human Genome Research Institute (U01HG007031, R21HG006187, U01HG004271, K99HG006698)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- transcript assembly, genome annotation, RNA-seq, cap analysis of gene expression, grit, Drosophila melanogaster, modENCODE, polyadenylation sites, alternative splicing, alternative promoters, automated annotation pipeline
- MeSH terms
- Animals, Chromosome Mapping, Drosophila melanogaster, RNA, Sequence Analysis, RNA, Genomics, Genome, Insect, Molecular Sequence Annotation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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