StaticSection Overview

Designed as an alternative to ChIP-seq, CUT&RUN is a method for efficiently mapping DNA-protein interactions. The 4DN CUT&RUN processing pipeline consists of trimming, alignment, filtering, visualization, and peak calling. The final outputs of the CUT&RUN pipeline are a bigWig signal track and peaks in bed format, both of which can be visualized in HiGlass.

The CUT&RUN Docker image, used in all steps of the pipeline, can be found at https://hub.docker.com/r/4dndcic/cut-and-run-pipeline