Tophat

Fast splice junction mapping for RNA-Seq reads with TopHat

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Requires Geneious 7.0+

    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 (included in this plugin), and then analyzes the mapping results to identify splice junctions between exons.This plugin runs on Mac OS and 64-bit Linux only, it is not supported Windows.

    Quick Start

    Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

    Once installed, run the plugin by selecting your reads and reference sequence then clicking on Align/Assemble - Map to Reference in the toolbar. TopHat is available as an option in the Algorithm drop-down menu.

    History

    7.2.1 (24 May 2017) – Download

    – Added debugging for a crash that would occur when a contig’s reference sequence name was not found in the input reference sequences’ names
    – Upgrade Bowtie2 to 2.3.2

    Citing

    Trapnell C, Pachter L, Salzberg SL, TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009 25(9):1105-1111.