ChIPseq

This pipeline was written for execution on the NYU big purple server. This readme describes how to execute the snake make workflow for paired-end ChIP-seq data pre-processing (fastq -> peak calling), Utilizing bowtie2 for alignment and MACS2 for peak calling. This pipeline assumes there is a control for each antibody sample (input or IgG). If there isn't, a common control can be duplicated in the samples_info.tab file for each antibody sample or some modification will have to made to this workflow to accomodate.

Description of files required for snakemake:

Snakefile

This file contains the work flow

samples_info.tab

This file contains a tab deliminated table with:

	1. The names of R1 and R2 of each fastq file as received from the sequencing center. 
	2. Simple sample names
	3. Condition (e.g. diabetic vs non_diabetic)
	4. Replicate #
	5. Sample name is the concatenated final sample_id 
	6. The antibody column specifies if the sample is the ChIP antibody or a control (input or IgG etc...)
	7. Additional metadata can be added to this table for downstream analysis

config.yaml

This file contains general configuaration info.

	1. Where to locate the samples_info.tab file
	2. Path to bowtie2 indexed genome

cluster_config.yml

Sbatch parameters for each rule in the Snakefile workflow

cat_rename.py

This script:

	1. Concatenates fastq files for samples that were split over multiple sequencing lanes
	2. Renames the fastq files from the generally verbose ids given by the sequencing center to those supplied in the Samples_info.tab file.
	3. The sample name, condition, and replicate columns are concatenated and form the new sample_id_Rx.fastq.gz files
	4. This script is executed snakemake_init.sh prior to snakemake execution

snakemake_init.sh

This bash script:

	1. loads the miniconda3/cpu/4.9.2 module
	2. Loads the conda environment (/gpfs/data/fisherlab/conda_envs/ChIPseq). You can clone the conda environment using the ChIPseq.yml file and modify this bash script to load the env.
	3. Executes snakemake

ChIPseq.yml

This file contains the environment info used by this pipeline.

FRP.py

This file computes the fraction of reads in peaks (FRP) and outputs a table with FRP, total fragments, and fragments within peaks.

Usage

When starting a new project:

	1. Clone the git repo using 'git clone --recurse-submodules https://github.com/mgildea87/ChIPseq.git'
	2. Run 'git submodule update --remote' to pull any changes that have been made to the cat_rename_init submodule.
	3. Within snakemake_init.sh specifiy the location of the sequencing files from the core. cat_rename.py will concatenate, rename, and copy these to a local directory 'fastq/' 
	4. Update the samples_info.tab file with fastq.gz file names and desired sample, condition, replicate names, and IgG control status
	5. Update config.yaml with path to bowtie2 indexed genome.
	6. Update cluster_config.yml with job desired specifications for each Snakemake rule, if desired.
	8. Perform a dry run of snakemake with 'snakemake -n -r' to check for errors and this will tell you the number of jobs required. You will need to load the miniconda3/cpu/4.9.2 module and activate the ChIPseq environment first. Dont forget to deactivate the environment and miniconda module before running snakemake_init.sh. This step is not necessary.
	9. Run 'bash cat_rename_init/snakemake_init.sh -c 'ChIPseq' -w 'ChIPseq' to execute workflow. The -c and -w parameters tell the workflow which conda env to use and which workflow is being executed.