A novel experimental and computational crosslinking and immunoprecipitation (CLIP) workflow called FAST-iCLIP (fully automated and standardized iCLIP), which reduces experimental time by ~50%, promises to improve research into RNA–protein interactions across human and pathogen RNAs. The researchers' aim was to address common limitations of CLIP investigations by improving the efficiency of sample preparation and extending analyses across protein-coding, non-coding and user-definable non-human transcriptomes. In addition, resulting data formats were standardized to facilitate comparisons between RNA-binding proteins. Application of FAST-iCLIP to the human and viral interactomes of poly(C)-binding protein 2 (PCBP2) revealed novel RNA–protein interactions and confirmed known functional protein roles. This pipeline should facilitate functional analyses of protein-coding and non-coding human transcriptomes, as well as the study of pathogen and microbiome interactomes.