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Bioinformatics Advance Access originally published online on March 16, 2009
Bioinformatics 2009 25(9):1105-1111; doi:10.1093/bioinformatics/btp120
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell 1,*, Lior Pachter 2 and Steven L. Salzberg 1

1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742 and 2Department of Mathematics, University of California, Berkeley, CA 94720, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites.

Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development.

Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu

Contact: cole{at}cs.umd.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Ivo Hofacker

Received on October 23, 2008; revised on February 24, 2009; accepted on February 26, 2009

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