hi-c-analysis's Introduction

Hi-C-Analysis

This repo discusses on dealing with Hi-c data and operations on the data. About Hi-C,it measures the frequency (as an average over a cell population) at which two DNA fragments physically associate in 3D space, linking chromosomal structure directly to the genomic sequence.

Introduction

The code covers on applying the below operations on Hi-c data:

Visualizing Hi-C data
Conversion of Hi-c sequence data to Hi-c Map using FANC
Analysis on Hi-c data

Setup

Linux/Unix setup:

Linux Environment setup

sudo apt-get update 

# make a new directory
mkdir hdf5-build
cd hdf5-build

# Downloading HDF5 files
wget https://support.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.10.5.tar.gz

# unpack
tar xzf hdf5-1.10.5.tar.gz
cd hdf5-1.10.5.tar.gz/

# use --prefix to set the folder in which HDF5 should be installed
# alternatively, you can omit --prefix=... here and run
# sudo make install to install globally (requires admin rights)
./configure --prefix=./hdf5-build
make
make install

export HDF5_DIR=/path/to/hdf5/dir


wget -O examples.zip "https://keeper.mpdl.mpg.de/d/147906745b634c779ed3/files/?p=/examples.zip&dl=1"
unzip examples.zip
cd examples


sudo apt install bowtie2

Python environment setup

pip install -r requirements.txt

Sequence to Map Conversion

For fastq sequences

fanc auto SRR4271982_chr18_19_1.fastq.gzip SRR4271982_chr18_19_2.fastq.gzip output/ \
          -g hg19_chr18_19.fa -i hg19_chr18_19/hg19_chr18_19 -n fanc_example -t 4 -r HindIII \
          --split-ligation-junction -q 30 --run-with test