Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression an
![Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks](https://cdn-ak-scissors.b.st-hatena.com/image/square/58011ff9a7d582c367ceac05c1149189b02629c6/height=288;version=1;width=512/https%3A%2F%2Fmedia.springernature.com%2Fm685%2Fspringer-static%2Fimage%2Fart%253A10.1038%252Fnprot.2012.016%2FMediaObjects%2F41596_2012_Article_BFnprot2012016_Fig1_HTML.jpg)