Running plot_figures script of the codes directory generates all the figures related to the analysis
The workflow folder contains the Snakemake environment with the necessary config file and Snakefile for running the Snakemake rules (workflow/rules folder) of the analyses (without normalization). The environment.yaml file listing the necessary packages is recommended for setting up the conda environment (e.g. conda env create -f environment.yaml ) before running. The workflow/index/mm10 folder must contain the bowtie2 indexed genome (mm10.*.bt2 formats). Multiple genomes can be provided in the analysis if different fastas are found in the config.yaml file. workflow/raw must contain the fastq pairs. If there are input files, samples and inputs in the workflow/raw folder should be named as "{couple}_chip.fastq.gz" and "{couple}_input.fastq.gz", respectively. Test fastq files are provided in the workflow/raw folder.
Our ChIP-Seq workflows ran under the versions below:
snakemake 7.26
fastqc 0.12.1
bowtie2 2.5.1
samtools 1.17
multiqc 1.14
picard 3.0.0
macs2 2.2.7.1
Python >3.8 and conda (e.g. version 24.1.2) are recommended.
The codes folder consists of the deepTools bash scripts used for the deeptools related visualizations.
Normalized bigwig files and peaks are stored here.