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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
- Bioinformatics
- RNA-Seq
- Genome
- Gene
- Transcription (genetics)
- Splice site
- Tuxedo Suite
- Bowtie (software)
- Cufflinks (software)
- Cuffdiff
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