Scripts required for the processing of FASTQ files (eg generating adjacency lists for Hi-C data)
- Python 2.7.12 or 3.6+
- Python 3.5.2 (required for iNPS in MNase-Seq pipeline)
- Python Modules:
- mg-tool-api
- numpy
- h5py
- scipy
- matplotlib
- TADbit
- pysam
- MACS2 - can be installed with pip, but runs on command line
- rpy2
- GEMtools
- HDF5
- Bowtie2
- BWA
- SAMtools
- BS-Seeker2
- libmaus2
- BioBamBam2
- imp (for 3D modelling with TADbit)
- mcl
- R (2.9.1)
- iNPS
For a guide to the full installation procedure the see ReadTheDocs.
Directly from GitHub:
.. code-block:: none :linenos:
cd ${HOME}/code
git clone https://github.com/Multiscale-Genomics/mg-process-fastq.git
cd mg-process-fastq
Create the Python environment
.. code-block:: none :linenos:
pyenv-virtualenv 2.7.10 mg-process-fastq pip install --editable .