Bioinformatics AdvancesBioinformaticsPeer-reviewed journal article
racoon_clip - a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data
Abstract
SummaryHere, 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 Implementationracoon_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). ContactKathi Zarnack, kathi.zarnack@bmls.de Issue SectionGenome analysis
- assay: CUT&Tag
- research focus: variant calling
- research focus: software / tool
- approach: statistical model
- approach: experimental assay
- Citations
- 3
- FWCI
- 0.41
- Field percentile
- top 47%
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