Here are some notes on processing RNA-seq data to find differentially expressed genes. A much abbreviated version of this pipeline comes from Cufflink’s Tutorial Page The extended version given below follows the more exploratory pattern of someone who hasn’t done much (any) NGS data analysis before. Tools Used TopHat v1.1.2 Cufflinks v1.0.1 Samtools v0.1.16 Requirements Sequence Files We are start