Bulk Epigenomics Pipeline - from FASTQ to Count Matrices

Snakemake pipelines to process FASTQ files from bulk epigenomics such as ChIP-seq, CUT&Tag, Chromatin Indexing. It can take as input Human samples (hg38), mouse samples (mm10) or PDX samples (hg38 for the tumor, mm10 for the mouse Tumor Micro Environment).
All the tools needed are embedded in a Singularity Environment, allowing you to run the pipeline in a containarized environment (see Singularity).

Command Line:

bash run_multiple_samples.sh ../sample_sheets/SampleSheet_CutTag_Human_Tumors.tsv $kdi/ChIP_seq/Test_bulkEpigenomics_CutTag_hT/

Set up & Requirements

1. Download pipeline

In order to set up the bulk Epigenomics pipeline, first download the github repository to a directory of your choice:

git clone git@github.com:vallotlab/bulk_Epigenomics

2. Download Singularity & Singularity Image

Then, download the Singularity Image at link comming soon, containing all the tools needed for each step of the package. This means you do not need any additional installation except :

• singularity (see Singularity)
• python3 (Python) and pandas python package (pandas)

3. Build Bowtie2 index & indicate path in design file

You need to have a bowtie2 index of either Human (hg38) or Mouse (mm10) genomes (see Bowtie2). In the species_design_configs.tsv, you'll need to modify all the bowtie2_index and second_species_bowtie2_index columns with the prefix towards the bowtie2 indexes.

4. Modify the launching script with your specific paths

You finally need to modify the run_multiple_samples.sh script changing:

• script_dir=~/GitLab/bulk_Epigenomics/ -> Path towards the downloaded repository
• image=~/Singularity/bulk_Epigenomics/bulkEpigenomics.sif -> Path towards the downloaded Image
• bind_directory=/data/ -> Root directory of the directory where the FASTQ files are located. This directory will be mounted in the container.
• cores=20 -> Number of cores you want to use

You are now set up and can move towards creating your sample sheet !

Launching the pipeline

Now copy and modify the 'SampleSheet_test_PE.csv' sample sheet for paired-end data or the 'SampleSheet_test_SE.csv' sample sheet for single-end data.

Note : the SampleSheet_template.csv is formatted for use on the Institut Curie HPC, and can be used to run the pipeline on output FASTQs from the KDI

Now launch the pipeline with the following command:

bash run_multiple_samples.sh ../sample_sheets/SampleSheet_CutTag_Human_Tumors.tsv $kdi/ChIP_seq/Test_bulkEpigenomics_CutTag_hT/