Christopher Cheshire
Christopher Cheshire

nf-core CUT&RUN - A comprehensive analysis pipeline for targeted antibody-based chromatin assays

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Christopher Cheshire, Charlotte West, Tamara Hodgetts

nf-core/CUT&RUN is a comprehensive analysis pipeline written in Nextflow that is designed to analyse data from experiments that target chromatin-bound proteins using antibodies; primarily CUT&RUN and CUT&Tag.

The pipeline is built around the principles of repeatability, reproducibility and transparency producing robust analysis with rich reporting at every stage. We have followed industry “test by design” standards when developing the pipeline with over 200 tests that verify the pipeline operation with every code change.

CUT&RUN/Tag experiments can be run with several different configurations such as with IgG controls, spike-ins and varying sample grouping scenarios. nf-core/CUN&RUN is designed to work in all of these configurations with easy-to-use parameterisation. Additionally, we provide multiple peak caller options with automatic IGV browser session generation.

nf-core CUT&RUN - A comprehensive analysis pipeline for targeted antibody-based chromatin assays

nf-core CUT&RUN - A comprehensive analysis pipeline for targeted antibody-based chromatin assays

Community
Christopher Cheshire
Christopher Cheshire
Christopher Cheshire

Christopher Cheshire

Post-doctoral Research Fellow at the Francis Crick Institute

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Poster presenter