I have transcript counts from RNA-seq data. There are three samples, and they are biological replicates of a cell line. My goal is to provide a ranked list of expressed genes, with some sort of expression quantifier for each gene/transcript.
I am wondering the best way to normalize the data - just calculate RPKM values and then remove outliers per transcript? Or should I perform some sort of upper quantile normalization? If so, what is the best way to do this?
Thank you for your help!