What does TopHat do?

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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. Because we are mapping mRNA with no introns to full genomes, TopHat then uses its parent program Bowtie to analyze the alignment results to identify splice junctions between exons and correctly aligns the reads. The mapped reads from TopHat saves as a BAM/SAM dataset.