CLIPper - CLIP peak enrichment recognition

A tool to detect CLIP-seq peaks.

Please visit our wiki page to learn more about usage of clipper: https://github.com/YeoLab/clipper/wiki/CLIPper-Home

Installation

# recreate PYTHON3 conda environment
cd clipper
conda env create -f environment3.yml
conda activate clipper3
pip install .

Alternative installation

1. Thanks @rekado for making clipper available at GNU Guix guix install clipper
2. We notice installation might be failing in some platform. Dockerized clipper is in the eclip repository here.

Command Line Usage

# shows all the options
clipper -h 

# minimal command
clipper -b YOUR_BAM_FILE.bam -o YOUR_OUT_FILE.bed -s hg19

Run test

cd clipper/clipper/test
python -m unittest discover

Right now the test coverage is still not 100%. And some subprocess warnings are not handled.

Frequently Asked Questions:

1. How do use additional reference genome? See here for instructions: Supporting additional species

2. Where can I use specify the Input bam file? Currently CLIPper does include input normalization. The input normalization pipeline is in another repository: Merge Peaks

Questions and suggestions

please open an issue in the repo.

Reference

Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol. 2009;16(2):130-137. doi:10.1038/nsmb.1545

Lovci MT, Ghanem D, Marr H, et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013;20(12):1434-1442. doi:10.1038/nsmb.2699