TopHat (bioinformatics)

TopHat is a bioinformatics software package that is used to align RNA-Seq reads to a genome in order to identify gene transcription start sites and splice sites. It is a component of the Tuxedo Suite, a comprehensive software package for RNA-Seq data analysis.

Overview

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Usage

TopHat is typically used in conjunction with other bioinformatics tools in the Tuxedo Suite, such as Cufflinks and Cuffdiff, to perform comprehensive analysis of RNA-Seq data. The typical workflow involves first aligning the RNA-Seq reads to the genome using TopHat, then assembling the transcripts using Cufflinks, and finally comparing gene and transcript expression levels using Cuffdiff.

Features

TopHat has several features that make it a powerful tool for RNA-Seq data analysis:

• Splice junction discovery: TopHat uses a novel algorithm to identify splice junctions, which allows it to accurately map reads that span splice junctions, even when the junctions are not annotated in the reference genome.

• Compatibility with Bowtie: TopHat uses the Bowtie aligner to perform the initial read mapping, which allows it to take advantage of Bowtie's speed and efficiency.

• Integration with the Tuxedo Suite: TopHat is designed to work seamlessly with the other tools in the Tuxedo Suite, which allows for a streamlined and comprehensive analysis of RNA-Seq data.

See also

• Bioinformatics
• RNA-Seq
• Genome
• Gene
• Transcription (genetics)
• Splice site
• Tuxedo Suite
• Bowtie (software)
• Cufflinks (software)
• Cuffdiff

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