This pipeline analyzes RNA-Seq data generated from Illumina TruSeq Stranded RNA prep kits. It first aligns the reads to a reference genome and then quantifies the transcripts based on a specified annotation using the Partek E/M method. The strand specificity is set to the Reverse – Forward option. The transcripts will then be filtered to exclude transcripts with low expression whose maximum raw read counts are less than or equal to 20 counts. Transcript read counts will be normalized using the Trimmed mean of M-values (TMM) algorithm.