Consider using Sierra Platinum for consensus peak calling on biological replicates

CCBR / CHAMPAGNE

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

https://ccbr.github.io/CHAMPAGNE/

MIT License

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Consider using Sierra Platinum for consensus peak calling on biological replicates #164

Open kelly-sovacool opened 6 months ago

kelly-sovacool commented 6 months ago

Müller, L., Gerighausen, D., Farman, M. et al. Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. BMC Bioinformatics 17, 377 (2016). https://doi.org/10.1186/s12859-016-1248-6

https://github.com/sierraplatinum/sierra

The tool is 9 years old and has no unit tests. We may want to rewrite it in Python.

kelly-sovacool commented 3 weeks ago

Also, there is minimal documentation for running the tool, and it appear to be a web server with a GUI... not ideal for our pipeline