TopHat: discovering splice junctions with RNA-Seq

C Trapnell, L Pachter, SL Salzberg - Bioinformatics, 2009 - academic.oup.com
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 …