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.
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
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
- 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
- For single hic file
fanc auto examples/test.hic ./example_output/