Clostridioides difficile is the major cause of nosocomial infections associated with antibiotic therapy. Despite being classified as an urgent Antibiotic Resistance Threat by the Centre for Disease Control and Prevention, its pathogenesis control is poorly understood. Previous studies have identified a number of non coding RNAs (ncRNAs) that may contribute to virulence of this important pathogen. Some of these ncRNAs regulate their targets by associating with their target messenger RNA to form an RNA duplex leading to modulation of mRNA translation and/or stability. To understand the mechanism of action of selected ncRNA candidates, we combine experimental and in silico approaches to identify their target genes. We first identified potential targets of the candidate ncRNAs using MAPS (MS2-affinity purification coupled with RNA-Seq). By adding an MS2 tag to an ncRNA of interest, this technique captures the complex formed by the ncRNA and its target RNAs. After purification of the captured complexes, the RNAs are sequenced for a differential analysis of the captures compared to a control condition with strain expressing untagged ncRNA and MS2 tag alone. In parallel, we used the IntaRNA bioinformatic tool to predict the interactions between candidate ncRNAs and mRNAs and ncRNAs expressed in C. difficiles . Sequence pairs with the lowest interaction energies were selected as the second set of duplexes between the ncRNA of interest and its RNA targets. Finally, the two sets of predicted ncRNA/mRNA pairs were integrated to propose the “best” potential ncRNA-target pairs. Resulting predictions are visualized as a circos graph. To perform these analyses, we have developed two snakemake pipelines that enable successive steps of MAPS data analysis to be carried out, and intaRNA predictions to be parallelized for faster execution times. By integrating the data from genome-wide experimental targets identification and in silico predictions as discussed in Georg J. et al. 2020, we were able to establish a list of several promising targets for selected ncRNA candidates for further functional validation by targeted experimental approaches.