khandaud15 / CUT-RUN

full pipeline to process the cut&run Data on slurm

CUT-RUN Analysis

Full pipeline to process the CUT&RUN Dataset on the uchicago Midway2/Midway3 cluster

Install all the tool required for running the workflow by creating anaconda environment

module load gcc
module load python
conda create -n cut_run
conda activate cut_run
conda install -c bioconda fastqc
conda install -c bioconda trimmomatic
conda install -c bioconda bowtie2
conda install -c bioconda samtools
conda install -c bioconda picard
conda install -c bioconda seacr
conda install -c bioconda bedtools
pip install deeptools

To run the script on the cluster, use the following command

sbatch cut_run.sh