This is is the ripseq pipeline from the Sequana project
| Overview: | pipeline dedicated to the analysis of RIP-seq (RNA ImmunoPrecipitation sequencing) |
|---|---|
| Input: | BigWig files |
| Output: | Candidates and G4 analysis |
| Status: | draft |
| Citation: | Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352 |
sequana_ripseq is a Snakemake pipeline dedicated to the analysis of RIP-seq (RNA ImmunoPrecipitation sequencing) experiments using precomputed coverage tracks (BigWig files). The pipeline identifies reproducibly enriched RNA regions by combining:
- replicate-to-replicate correlation metrics,
- IP vs INPUT signal comparison,
- gene annotation,
- optional G-quadruplex detection using G4Hunter implementation in Sequana.
The workflow operates on sliding genomic windows and reports candidate regions showing: high correlation between IP replicates (CIP), sufficient IP signal intensity, enrichment compared to INPUT controls.
sequana_ripseq is based on Python3, just install the package as follows:
pip install sequana_ripseq --upgrade
sequana_pipelines_ripseq --help sequana_pipelines_ripseq --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd ripseq sh ripseq.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:
snakemake -s ripseq.rules -c config.yaml --cores 4
This pipelines requires Sequana and its dependencies including pyBigWig and no third-party tools
- Designed for experiments with 4 replicates per condition
- Supports multiple cases (e.g. 24h / 48h / Mock)
- Correlation-based strategy increases robustness to noisy IP signal
- Integration with G4Hunter enables structural RNA analysis
Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
| Version | Description |
|---|---|
| 0.0.1 | First release. |
To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.