TopHat: discovering splice junctions with RNA-Seq
By Cole Trapnell, Lior S. Pachter, Steven L. Salzberg. Bioinform., 2009
1,854 citations recorded by the source corpus.
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@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/16a7b77a961422e3f91ee7e88efe1a79ec2f75e1
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In Molecular Biology
- Aaron T. L. Lun
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- Fritz J. Sedlazeck
- Todd J. Treangen
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- Brian J. Haas
Citations in the corpus
- A Longitudinal Big Data Approach for Precision Health (2019, positive): “The TopHat package 76 was used to align the reads to personal genomes, followed by HTseq (v.0.6.1) and DESEQ2 (v.3.5) 77 for transcript assembly and RNA expression quantification.”
- Lessons from the cancer genome. (2013, neutral): “of foreign DNA (such as from viruses) (Beroukhim et al., 2007; Chen et al., 2009; Cibulskis et al., 2013; Dees et al., 2012; Kim and Salzberg, 2011; Kostic et al., 2011; Trapnell et al., 2009).”
- Structural variant calling: the long and the short of it (2019, methodology): “One of the earliest fusion detection methods was TopHat-Fusion [56], which used a specialized version of TopHat [91].”