Welcome to racoon_clip’s documentation!
Contents:
Note
This project is under active development.
racoon_clip - What is it?
racoon_clip processes your iCLIP and eCLIP data from raw files to single-nucleotide crosslinks in a single step. It is an automatition of the iCLIP pipeline pubished by Busch et al. 2020 (iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites) making the same processing now availabe 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.
Steps performed by racoon_clip.
Usage
Once installed you can run racoon with:
racoon_clip run --cores <number_of_cores> --configfile </path/to/config/file.yaml>
Requirements
python >3.9
conda or mamba
pip