Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

An HMM-based domain caller from bw

Paired-end CUT and RUN data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, Bowtie 2, SEACR, MultiQC

Tools to call large binding domains from CutAndRun-seq or to identify long non-coding RNA transcripts from RNA-seq