High throughout sequencing technologies are now allowing us to interrogate intermediate layers of gene expression from nascent transcription to translation. At the same time, new sequencing protocols can help to determine where RNA-binding proteins interact with target transcripts and control these different layers of post-transcriptional gene regulation. These new protocols require and motivate dedicated computational approaches to analyze the resulting noisy data. I present our recent and ongoing projects to identify and analyze interactions of RNA-binding proteins and ribosomes on coding and non-coding transcripts.