Before you begin

Have a copy of the HiChIP scripts on your machine:

Clone this repository:

git clone https://github.com/dovetail-genomics/HiChiP.git

And make the enrichment_stats.sh script executable:

chmod +x ./HiChiP/enrichment_stats.sh

Dependencies

Make sure that the following dependencies are installed:

• pysam

• tabulate

• bedtools

• deeptools

• matplotlib

• pandas

• numpy

• bwa

• pairtools

• samtools

If you are facing any issues with the installation of any of the dependencies, please contact the supporter of the relevant package.

python3 and pip3 are required, if you don’t already have them installed, you will need sudo privileges.

• Update and install python3 and pip3:

sudo apt-get update
sudo apt-get install python3 python3-pip

• To set python3 and pip3 as primary alternative:

sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 1
sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1

If you are working on a new machine and don’t have the dependencies, you can use the installDep.sh script in this repository for updating your instance and installing the dependencies and python3. This process will take approximately 10’ and requires sudo privileges. The script was tested on Ubuntu 18.04 with the latest version as of 04/11/2020

If you choose to run the provided installation script you will first need to set the permission to the file:

chmod +x ./HiChiP/installDep.sh

And then run the installation script:

./HiChiP/installDep.sh

Remember!

Once the installation is completed, sign off and then sign back to your instance to refresh the database of applications.

Input files

For this tutorial you will need:

• fastq files R1 and R2, either fastq or fastq.gz are acceptable

• reference in a fasta file format, e.g. hg38

• peak calls from ChiP-seq experiment (e.g. your own experiment or ENCODE gold standard in bed or narrowpeak format, as explained here), more details and links to ENCODE files can be found here.

If you don’t already have your own input files or want to run a test on a small data set, you can download sample fastq files from the HiChIP Data Sets section. The 2M data set is suitable for a quick testing of the instructions in this tutorial.

The following files are suitable for testing, you can download them as follows:

wget https://s3.amazonaws.com/dovetail.pub/HiChIP/fastqs/HiChiP_CTCF_2M_R1.fastq.gz
wget https://s3.amazonaws.com/dovetail.pub/HiChIP/fastqs/HiChiP_CTCF_2M_R2.fastq.gz
wget https://www.encodeproject.org/files/ENCFF017XLW/@@download/ENCFF017XLW.bed.gz

For zipped bed files, unzip them after download is completed (no need to unzip fastq.gz files)

Example:

gunzip ENCFF017XLW.bed.gz