What does TopHat do?
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Revision as of 15:15, 6 February 2018 by Macampbell (talk | contribs) (Created page with "'''TopHat''' aligns RNA-seq reads to mammalian-sized genomes (in our case, to the mm10 mouse genome build). Because we are using paired-end datasets, forward and reverse, we n...")
TopHat aligns RNA-seq reads to mammalian-sized genomes (in our case, to the mm10 mouse genome build). Because we are using paired-end datasets, forward and reverse, we need to set a mean inner distance or the average distance in basepairs between reads. TopHat then uses its parent program Bowtie to analyze the alignment results to identify splice junctions between exons.
