The Concepts of Mean Fragment Length and Effective Length in RNA Sequencing

Last time we examined why we need to adjust for length in order to compare relative abundances during within-sample normalization. Today we will take one step forward in understanding how we accomplish this. Before we can perform normalization on the counts we need to calculate an effective length which is dependent on the mean fragment length. Here we describe what the mean fragment length represents and how to calculate the effective length for an RNA sequencing experiment.