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Nat Biotechnol. 2014 Apr;32(4):341-6. doi: 10.1038/nbt.2850. Epub 2014 Mar 16.

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

Author information

1
Department of Biostatistics, University of California at Berkeley, Berkeley, California, USA.
2
Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
3
1] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [2].
4
1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2].
5
1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [3].

Abstract

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.

PMID:
24633242
PMCID:
PMC4037530
DOI:
10.1038/nbt.2850
[Indexed for MEDLINE]
Free PMC Article

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