RIPseq-analysis-workflow

Summarized existing analysis methods for RIP-seq, including alignment, peak calling, and annotation.

analysis-workflow

1. fastqc
2. create index & sequence
3. duplicated & make index
4. peak calling
5. annotation

peak calling methods

1. CLAM

https://github.com/Xinglab/CLAM

installation

conda activate python2.7
pip install --index-url https://test.pypi.org/simple/ --no-deps CLAM

2. Piranha

https://github.com/smithlabcode/piranha

installation

conda activate python2.7
conda install -c bioconda piranha

3. RIPSeeker

https://bioconductor.riken.jp/packages/3.4/bioc/html/RIPSeeker.html

https://github.com/yueli-compbio/RIPSeeker