Welcome to racoon_clip’s documentation!
What is racoon_clip?
racoon_clip processes your iCLIP and eCLIP data from raw files to single-nucleotide crosslinks in a single step. It is an automation of the iCLIP pipeline published by Busch et al. 2020 (iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites) making the same processing now available for both iCLIP and eCLIP data in a highly reproducible manner.
The performed steps are a quality filter (optional), demultiplexing (optional), adapter trimming, genome alignment, deduplication (optional) and selection of single nucleotide crosslinks. For details on the performed steps please see Detailed description of steps performed by racoon.
Schema of workflow:
Supported CLIP experiments
iCLIP, iCLIP2, iCLIP3
eCLIP, seCLIP
miR-eCLIP
custom set-ups for other CLIP experiments based on read-stops
Set-up of reads, obtained from different types of CLIP experiments:
Usage
racoon_clip consists of two main commands:
racoon_clip crosslinks --cores <number_of_cores> --configfile </path/to/config/file.yaml>
racoon_clip peaks --cores <number_of_cores> --configfile </path/to/config/file.yaml>
Use crosslinks for crosslink identification and peaks for peak calling. Check the tutorial to find out what needs to be in your config.yaml file.
Requirements
conda
python =3.9.0
mamba >= 1.3.1
or Docker / Apptainer (SingularityCE is not supported)
Citations
Klostermann & Zarnack 2024 – racoon_clip—a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data
Busch et al. 2020 – iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
Huppertz et al. 2014 – iCLIP: protein-RNA interactions at nucleotide resolution