CLIPittyClip: a single-command framework for CLIP sequencing data analysis

Crosslinking immunoprecipitation (CLIP) sequencing is the standard method for mapping RNA-binding protein (RBP) binding sites transcriptome wide, yet most analysis pipelines are either modular toolkits requiring manual assembly or large-scale workflows built for consortium infrastructure. Here, we present CLIPittyClip, a single-command pipeline that processes CLIP data from raw FASTQ files to a peak matrix and crosslink site outputs, supports five major CLIP read architectures and runs entirely locally on standard laptop hardware. The pipeline introduces CLink, a Python reimplementation of CLIP Tool Kit crosslink-induced truncation and mutation site analyses that is up to 27-fold faster while recovering equivalent binding motifs and crosslink site resolution. Using CLIP data for a prototypical RBP, we performed systematic parameter sweeps for two peak callers to establish empirically calibrated defaults for the pipeline. We validated CLIPittyClip against published ELAVL1, HNRNPC, and RBFOX2 datasets spanning BrdU-CLIP, iCLIP, eCLIP, and PAR-CLIP architectures, and confirmed compatibility with downstream analyses for differential binding and motif analysis. CLIPittyClip provides a fast, local, and practical processing layer for CLIP data analysis in a single-lab setting and is freely available at https://github.com/LunaRNALab/CLIPittyClip.