Rnnotator: A Tool for Assembling RNA-Seq Data
Author Information
Author(s): Martin Jeffrey, Bruno Vincent M, Fang Zhide, Meng Xiandong, Blow Matthew, Zhang Tao, Sherlock Gavin, Snyder Michael, Wang Zhong
Primary Institution: Lawrence Berkeley National Laboratory
Hypothesis
Can RNA-Seq data be assembled into full-length transcripts without a reference genome?
Conclusion
Rnnotator can accurately reconstruct full-length transcripts from RNA-Seq data even in the absence of a complete reference genome.
Supporting Evidence
- Rnnotator produced highly accurate contigs with 95% accuracy.
- The pipeline reconstructed full-length genes for 54.3% of existing gene models.
- Rnnotator discovered many novel transcribed regions absent from well-annotated genomes.
Takeaway
Rnnotator is a computer program that helps scientists put together pieces of genetic information from RNA without needing a complete map of the genes.
Methodology
Rnnotator processes RNA-Seq data by filtering, assembling, and post-processing to create transcript models.
Limitations
Rnnotator may struggle with poorly expressed genes and cannot resolve transcripts from duplicated regions or polymorphic alleles.
Digital Object Identifier (DOI)
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