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TopHat is a fast splice junction mapper for RNA-Seq data. More advanced TopHat2 options can be found in its manual, or by typing: $ tophat2 -h. TopHat uses Bowtie to map RNA-seq reads to a reference genome, then analyzes the Check the TopHat manual for more details of the available options. By first mapping RNA-Seq reads to the genome, TopHat identifies potential exons See the Getting started guide for detailed instructions about installing TopHat is a fast splice junction mapper for RNA-Seq reads. See the Puhti user guide for more information about running batch jobs. TopHat (biotools:tophat) ID Verified · OpenEBench. ccb.jhu.edu/software/tophat/index. ccb.jhu.edu/software/tophat/manual.shtml User manual. Guides and videos. Getting started. Introduction to Tophat. This manual explains the elements on the Tophat map as well as how to get started using Tophat. ccb.jhu.edu/software/tophat/manual.shtml User manual TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and Improved support for adding unpaired reads to PE reads in the same TopHat2 run (please see the manual entry for this usage). TopHat is a fast splice junction mapper for RNA-seq reads. It aligns RNA-seq reads to TopHat documentation: tophat.cbcb.umd.edu/manual.htmlAlignment / TopHat2 for paired-end reads. Description. This tool aligns Illumina paired end RNA-seq reads to publicly available genomes.