Dear Biostars community, I am a beginner in bioinformatics analysis with a PhD in molecular biology, currently studying MSc data science with computational biology concentration and aiming to make a career transition to work with big data in the biomedical field. I have recently started a collaboration with a research group in order to get project experience. My aim is to identify genome-wide targets of a snoRNA by means of PARIS (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821472/). I have been messing around with different tools in order to detect hybrid RNAs but I am not confident in my approach. After adapter and quality trimming of the paired-end reads (Trimmomatic), I have merged them (BBmerge) and subsequently aligned them (STAR) to the whole human genome (primary assembly index). However, the results from the alignment are bad (only 0.5%) and I am not sure how to analyse the outcome. Basically, I want to know which RNA is bound to my target RNA on the left or right arm of the sequenced hybrids respectively. I would be grateful to any suggestions on how to analyse these kind of experiments in terms of tools and procedure. Many thanks and best wishes, Christina