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macs2_vs_genrich_atac_options's Introduction

macs2_ATAC_options

This code is to acitvate and run conda enviorments to determine the cut sites or the mononucleosomes of ATAC-seq peaks and remove any blacklist peaks

Install macs

required: https://anaconda.org/bioconda/macs2

conda create -n macs2

conda activate macs2

conda install -c bioconda/label/cf201901 macs2 

conda deactivate

Install bedtools

required: https://anaconda.org/bioconda/bedtools

conda create -n bedtools

conda activate bedtools

conda install -c bioconda/label/cf201901 bedtools 

conda deactivate

Blacklist peaks hg19

required: https://www.encodeproject.org/annotations/ENCSR797MUY/

Genrich_ATAC_options

Install Genrich

required: https://anaconda.org/bioconda/genrich

conda create -n Genrich

conda activate Genrich

conda install -c bioconda genrich

conda deactivate

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