Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., ... & Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols, 7(3), 562-578.
总之这套流程过时了,但是可以作为一个参考。