Dear all,

We are currently planning an extensive experiment of a time-course involving ribosome profiling, which we would like to investigate in terms of changes in translational kinetics, possibly via WGCNA. Since ribosome profiling requires two separate measurements for mRNA levels and corresponding ribosome footprints, we were wondering how to supply these two measurements to WGCNA. What is currently done in many papers is to divide the footprint counts per gene by the corresponding mRNA-seq read counts, however, this so-called "translation efficiency" measure seems arbitrary given that it assumes an almost perfect comparability between both protocols. Thus, an alternative solution would be most welcome.

Any comments or recommendations are greatly appreciated!