Identification of Novel Transcripts in Annotated Genomes Using RNA-Seq

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2011 Jun 24

PMID 21697122

Citations 588

Authors

Adam Roberts

Harold Pimentel

Cole Trapnell

Lior Pachter

Affiliations

Soon will be listed here.

Abstract

Summary: We describe a new 'reference annotation based transcript assembly' problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation.

Availability: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license.

Contact: cole@broadinstitute.org; lpachter@math.berkeley.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.

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