ArticleBioinformatics advances2024
racoon_clip-a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data.
Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
4 citing papers in PubMed.
- Isotope-free mapping of protein-RNA interactions at single-nucleotide resolution by iCLIP3.STAR protocols · 2026Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data.Bioinformatics (Oxford, England) · 2026Article
- A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: A vast variety of biological questions connected to RNA-binding proteins can be tackled with UV crosslinking and immunoprecipitation (CLIP) experiments. However, the processing and analysis of CLIP data are rather complex. Moreover, different types of CLIP experiments like iCLIP or eCLIP are often processed in different ways, reducing comparability between multiple experiments. Therefore, we aimed to build an easy-to-use computational tool for the processing of CLIP data that can be used for both iCLIP and eCLIP data, as well as data from other truncation-based CLIP methods. Results: Here, we introduce racoon_clip, a sustainable and fully automated pipeline for the complete processing of iCLIP and eCLIP data to extract RNA binding signal at single-nucleotide resolution. racoon_clip is easy to install and execute, with multiple pre-settings and fully customizable parameters, and outputs a conclusive summary report with visualizations and statistics for all analysis steps. Availability and implementation: racoon_clip is implemented as a Snakemake-powered command line tool (Snakemake version ≥7.22, Python version ≥3.9). The latest release can be downloaded from GitHub (https://github.com/ZarnackGroup/racoon_clip/tree/main) and installed via pip. A detailed documentation, including installation, usage, and customization, can be found at https://racoon-clip.readthedocs.io/en/latest/. The example datasets can be downloaded from the Short Read Archive (SRA; iCLIP: SRR5646576, SRR5646577, SRR5646578) or the ENCODE Project (eCLIP: ENCSR202BFN).
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.