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TopHat
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 needs Bowtie to run. Before you can use TopHat you must initialize both TopHat and Bowtie by giving the command:
module load bowtie
After that you can start TopHat by giving command:
tophat
