PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data.

Abstract

RNA-protein interactions play essential roles in every living organism, with RNA transcription, processing, and translation being just a few examples. Therefore, determining the set of RNAs that are bound by individual RNA-binding proteins, as well as the precise location of the interaction, is crucial for biological understanding. CLIP (UV-cross-linking and immunoprecipitation) is a method developed to study these interactions. Several variations of the CLIP protocol have been developed, e.g. iCLIP (individual-nucleotide resolution CLIP), which offers nucleotide-precise resolution of the cross-linking event. PARANOiD is a versatile software for fully automated analysis of iCLIP and iCLIP2 data. It contains all steps necessary for preprocessing, the determination of cross-link locations, and several additional steps, which can be used to detect specific characteristics, e.g. definite distances between cross-link events or identify binding motifs. Additionally, results are visualized as statistical plots for a quick overview and as standardized bioinformatics file formats, which can be used for further analysis steps. PARANOiD is published under the MIT license and is available from https://github.com/patrick-barth/PARANOiD. The documentation is available at https://paranoid.readthedocs.io/en/latest/index.html.